/* subutil.h * >> Set tabs to 4 spaces for a nice printout * * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * File Name: subutil.h * * Author: James Ostell * * Version Creation Date: 11/3/93 * * $Revision: 6.39 $ * * File Description: Utilities for creating ASN.1 submissions * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * $Log: subutil.h,v $ * Revision 6.39 2001/12/12 16:01:47 kans * added MOLECULE_TYPE_TRANSCRIBED_RNA, SUBSRC_transgenic, SUBSRC_environmental_sample, and SUBSRC_isolation_source * * Revision 6.38 2001/12/11 16:50:41 kans * added TpaAssembly user object creation functions * * Revision 6.37 2001/12/10 13:47:44 kans * added MOLECULE_TYPE defines for CRNA and SNORNA * * Revision 6.36 2001/11/09 15:12:21 kans * moved collaborator to separate function per user object * * Revision 6.35 2001/11/09 13:21:08 kans * added collaborator field to reftrack user object * * Revision 6.34 2001/11/09 12:54:47 kans * added model evidence user object functions * * Revision 6.33 2001/07/29 16:23:58 kans * added AddOrganismToEntryEx to allow entry of taxonID * * Revision 6.32 2001/01/25 19:55:14 kans * added AddGenBankSetToSubmission for patents and other bulk submissions of unrelated sequences * * Revision 6.31 2000/11/15 23:18:00 kans * gene ontology user object functions * * Revision 6.30 2000/10/10 15:06:01 kans * added SUBSRC_endogenous_virus_name * * Revision 6.29 2000/09/28 11:41:33 ostell * added GENOME_endogenous_virus * * Revision 6.28 2000/09/20 12:32:54 kans * removed AddMethodToRefGeneTrackUserObject and AddSupportToRefGeneTrackUserObject * * Revision 6.27 2000/08/29 22:27:02 kans * reftrack support now has organism field * * Revision 6.26 2000/07/21 10:54:14 kans * added functions for adding Method and Support to RefGeneTrack user object * * Revision 6.25 2000/07/12 22:45:15 kans * added ORGMOD_old_lineage * * Revision 6.24 2000/06/20 17:17:28 kans * added orgmod.subtype authority through breed * * Revision 6.23 2000/06/14 16:41:20 kans * added SUBSRC_segment * * Revision 6.22 2000/03/10 18:35:46 kans * added CreateContigCloneUserObject for genome contig RefSeq records * * Revision 6.21 2000/02/26 23:55:34 kans * added AddPhrapGraphToSeqLit, using internal extended SeqLit to track, readjust graphs to current position of seqlit in delta seq - may need to move fields to public SeqLit if problems arise * * Revision 6.20 2000/02/24 23:15:00 kans * added AddSecondaryAccnToEntry * * Revision 6.19 2000/02/23 19:25:54 kans * AddFakeGapToDeltaSeq returns SeqLitPtr so program can set fuzz after SpreadGapsInDeltaSeq is no longer being called * * Revision 6.18 2000/02/23 18:28:39 kans * added AddFakeGapToDeltaSeq to set fuzz even if nonzero length is passed in * * Revision 6.17 2000/02/07 16:48:08 ostell * added AddDeltaSeqToNucProtEntry() * * Revision 6.16 1999/12/20 19:57:45 kans * added AddStatusToRefGeneTrackUserObject * * Revision 6.15 1999/12/14 17:32:45 ostell * changed protoplast to proplastid * * Revision 6.14 1999/10/05 20:36:01 kans * added more GENOME_ types (JO) * * Revision 6.13 1999/08/05 20:43:44 kans * added CreateSubmissionUserObject (JP) * * Revision 6.12 1999/03/17 22:49:38 kans * changed SUBSOURCE_ to SUBSRC_ * * Revision 6.11 1999/03/17 20:04:40 kans * added SUBSOURCE_ and ORGMOD_ defines * * Revision 6.10 1998/10/02 17:48:12 kans * new parameters to AddAccessionToRefGeneTrackUserObject, and added CreateMrnaProteinLinkUserObject * * Revision 6.9 1998/09/29 15:34:20 kans * added comment for new choices in molinfo.completeness * * Revision 6.8 1998/09/23 16:41:49 kans * removed from and to from AddAccessionToRefGeneTrackUserObject * * Revision 6.7 1998/08/20 20:37:00 kans * add comment parameter to reftrack user object function * * Revision 6.6 1998/08/11 22:27:26 kans * added CreateRefGeneTrackUserObject and AddAccessionToRefGeneTrackUserObject * * Revision 6.5 1998/02/05 19:19:30 kans * added AddPhrapGraph * * Revision 6.4 1998/01/06 03:29:49 ostell * added AddGeneticCodetoEntry() * * Revision 6.3 1997/12/15 17:31:48 kans * backed out accidental checkin * * Revision 6.1 1997/11/25 20:56:04 ostell * GENOME_genomic changed from 2 to 1 * * Revision 6.0 1997/08/25 18:07:39 madden * Revision changed to 6.0 * * Revision 5.12 1997/07/11 18:23:29 kans * added Add[Pop/Phy/Mut]SetToSubmission * * Revision 5.11 1997/06/19 18:39:13 vakatov * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization * * Revision 5.10 1997/05/16 19:14:03 ostell * moved prototype of NewDescrOnSeqEntry from subutil.c to subutil.h to make * it external. * * Revision 5.9 1997/03/17 17:18:46 tatiana * added defines for BioSource.genome * * Revision 5.8 1996/10/16 18:10:56 epstein * change C++ right paren to brace per Eric Hackborn * * Revision 5.7 1996/09/05 20:20:28 ostell * added CitSubUpdateBuild() * * Revision 5.6 1996/09/04 22:33:06 ostell * added MakeCommentFeature() * * Revision 5.5 1996/08/20 15:32:53 tatiana * prototypes added for AddAAsToByteStore and AddBasesToByteStore * * Revision 5.4 1996/06/14 19:00:06 ostell * fixed line wraps * * Revision 5.3 1996/06/14 18:07:38 ostell * added AddOrgModToEntry() and AddSubSourceToEntry() * * Revision 5.2 1996/06/14 17:27:18 ostell * added comments to subutil on BioSource and MolInfo attributes * * Revision 5.1 1996/06/13 03:34:53 ostell * added support for delta seqs and submittor_key * fixed memory leak in AddAminoAcidsToBioseq() * * Revision 5.0 1996/05/28 13:23:23 ostell * Set to revision 5.0 * * Revision 4.2 1996/03/05 17:06:25 tatiana * remove static from GetDescrOnSeqEntry, * taxonomy added to AddOrganismToEntryNew arguments * * Revision 4.1 1996/01/31 02:35:00 ostell * added AddCodeBreakToCdRegion() and AddAntiCodonTotRNA() * * Revision 4.0 1995/07/26 13:49:01 ostell * force revision to 4.0 * * Revision 1.8 1995/07/25 17:49:32 kans * added prototype for AddOrganismToEntryNew * * Revision 1.7 1995/07/25 14:48:17 tatiana * add new functions for Biosource and Molinfo * * Revision 1.6 1995/06/03 13:45:47 ostell * changes made in valid to use gather functions and ErrPostItem instead * of previous custom functions * * Revision 1.5 1995/05/15 21:46:05 ostell * added Log line * * * * ========================================================================== */ #ifndef _NCBI_SubUtil_ #define _NCBI_SubUtil_ #ifndef _NCBI_Submit_ #include #endif #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { #endif /***************************************************************************** * * Create a GenBank direct submission * This supports a basic set of datatypes for making a new direct * submission to GenBank in ASN.1. It is designed for folks wanting to * read their own data storage format, then make a valid direct submission * without going through an intermediate tool. * * You may have many "entries" in a single submission. A single entry * may contain: * One protein sequence (called a "Bioseq") * One nucleic acid sequence (called a "Bioseq") * One nucleic acid sequence for which you only have a series of * sequence pieces (e.g. you sequenced around the exons of a * genomic sequence, but not the introns) (called a "segmented * set") * One nucleic acid sequence and the protein sequences it codes for. * (nucleic acid may a a single Bioseq or a segmented set) * (this entry called a "nuc-prot set") * * NCBI considers the protein sequences part * of the submission, and they are created as proteins in their own right * by the routines below. You can either supply the protein sequence from * your own software (best case), in which we check that the coding region * you supply translates to it. If you do not supply a protein sequence, * then all we can do is check that it translates without stops. * * NCBI also considers "gene" to refer to a region of nucleic acid * within which are found elements (such as promoters, coding regions,etc) * leading to a phenomenon recognized as a gene (note this also accomodates * anonymous markers as well as expressed products). This is in contrast to * so other notions that a gene is simply a qualifier on other features of * the DNA. A separate function to produce a gene feature is supplied. The * intervals given for it should include the intervals for the other * features it contains. * * The process of building the direct submission is roughly: * * Create the submission * Add the submission citation * Create an entry (can be 1 or more sequences) * Add the organism information * Add any publication citations * Add the sequences * Fill in the residues * Add the features * Validate the entry * Write the entry * Free the memory used * * Each element may have subfunctions: * * Create a citation * Add author names * Add author affiliation * * Create a sequence * Add modifiers * * Create a feature * Add information specific to type of feature * Add intervals on the sequence * *****************************************************************************/ typedef Boolean (* SubErrorFunc) (CharPtr msg); typedef struct ncbisub { SeqSubmitPtr ssp; /* the submission */ SubErrorFunc err_func; /* the error handler */ Int2 gap_count; /* for unique gap names in segs */ CharPtr submittor_key; /* used for turning local SeqId to General */ } NCBISub, PNTR NCBISubPtr; #define PubPtr ValNodePtr /* should really be typedeffed */ /***************************************************************************** * * Prototypes for building a direct submission * *****************************************************************************/ /* default error handler */ NLM_EXTERN Boolean DefaultSubErrorFunc (CharPtr msg); /***************************************************************************** * * Create/Free the NCBISub * *****************************************************************************/ NLM_EXTERN NCBISubPtr NCBISubCreate ( CharPtr last_name, CharPtr first_name, CharPtr middle_name, CharPtr initials, /* separated by periods, no initial for last name */ CharPtr suffix, /* Jr. Sr. III */ CharPtr affil, /* e.g. "Xyz University" */ CharPtr div, /* e.g. "Dept of Biology" */ CharPtr street, /* e.g. "123 Academic Road" */ CharPtr city, /* e.g. "Metropolis" */ CharPtr sub, /* e.g. "Massachusetts" */ CharPtr country , /* e.g. "USA" */ CharPtr postal_code, /* e.g."02133" */ CharPtr phone , CharPtr fax , CharPtr email, Boolean hold_until_publish , Int2 release_month , Int2 release_day , Int2 release_year ); NLM_EXTERN Boolean DefineSubmittorKey( NCBISubPtr nsp, CharPtr submittor_key ); /* submitting large scale lab, for regular submissions */ /**** WARNING: NCBISubBuild() is the old style submission ***/ /**** It has been replaced by NCBISubCreate() ***/ /**** NCBISubBuild will be discontinued ***/ NLM_EXTERN NCBISubPtr NCBISubBuild ( CharPtr name, CharPtr PNTR address , CharPtr phone , CharPtr fax , CharPtr email, Boolean hold_until_publish , Int2 release_month, Int2 release_day, Int2 release_year ); /** every submission must have 1 submission citation **/ /** see below to add authors and affiliation **********/ NLM_EXTERN Boolean CitSubForSubmission ( NCBISubPtr submission, PubPtr cit_sub ); NLM_EXTERN Boolean AddToolToSub ( NCBISubPtr nsp, CharPtr tool ); NLM_EXTERN Boolean AddCommentToSub ( NCBISubPtr nsp, CharPtr comment ); NLM_EXTERN Boolean AddTypeToSub ( NCBISubPtr nsp, Uint1 type ); NLM_EXTERN Boolean NCBISubWrite ( NCBISubPtr ssp, CharPtr filename ); NLM_EXTERN NCBISubPtr NCBISubFree ( NCBISubPtr ssp ); /***************************************************************************** * * You can (should) run the ncbi validator routines on your final submission. * It returns a count of all errors or questions found. * * The errfile parameter is no longer supported. Errors are directed * based on the ErrLog functions in the toolkit. If you have done none * of this, then errors will appear on stderr. * *****************************************************************************/ NLM_EXTERN Int2 NCBISubValidate (NCBISubPtr nsp, FILE * errfile); /***************************************************************************** * * Add Entries to the Submission * Add Sequences to the Entries * *****************************************************************************/ /***************************************************************************** * * About Sequence Identifiers: * * Note that in all functions below where you create a Bioseq in your entry, * you can supply a number of different pieces of information to make a * sequence id. * * local_name: This is a string for whatever name you call this sequence * locally. Could be a clone name or whatever. There are no * limits on this other than it should be unique in the * submission. It is REQUIRED. * * SeqEntryPtr: Returned by the function, this is a pointer to the Bioseq. * * In later functions, such as adding feature locations, you can refer to * the Bioseq you created either with the local_name or directly with the * SeqEntryPtr. Whatever is more convenient for you is fine. * * The other ids only apply to updates. These allow you to update your * entry in GenBank simply by sending a new entry with the same accession * number you were issued on the last one. In this case you should also * be sure to add the create_date, which will be returned to you in the * ASN.1 of your direct submission after processing. This is not absolutely * required, but does let us check that it is the right entry (errors * could occur when you enter your old accession number). * * genbank_locus: OPTIONAL on update. The name appearing on the LOCUS line. * genbank_accession: REQUIRED on update. * gi_number: OPTIONAL on update for now. The unique ID assigned by NCBI * to a particular sequence (DNA or protein) in your entry. * * If you update your entry, whether you change the sequence or not, the * accession number and locus will remain the same, so people can retrieve * your new data with the old id. However, the gi_number is explicitly keyed * to the sequence, and will change if there are any changes/additions to * the sequence. In addition, a history will be created indicating the old * gi_number and the date the new entry replaced it. Both old and new * entries will be available from NCBI for retrieval on gi_number. Only the * new entry will appear in the next GenBank or Entrez release. * *****************************************************************************/ /*** Entry contains only 1 raw Bioseq ***/ NLM_EXTERN SeqEntryPtr AddSeqOnlyToSubmission ( NCBISubPtr submission , CharPtr local_name , CharPtr genbank_locus , CharPtr genbank_accession , Int4 gi_number , Int2 molecule_class, Int2 molecule_type , Int4 length , Int2 topology , Int2 strandedness ); /*** Entry contains a segmented set of Bioseqs ***/ NLM_EXTERN SeqEntryPtr AddSegmentedSeqToSubmission ( NCBISubPtr submission , CharPtr local_name , CharPtr genbank_locus , CharPtr genbank_accession , Int4 gi_number , Int2 molecule_class, Int2 molecule_type , Int4 length , Int2 topology , Int2 strandedness ); NLM_EXTERN SeqEntryPtr AddSeqToSegmentedEntry ( NCBISubPtr submission, SeqEntryPtr segmented_seq_entry, CharPtr local_name , CharPtr genbank_locus , CharPtr genbank_accession , Int4 gi_number , Int2 molecule_class, Int2 molecule_type , Int4 length , Int2 topology , Int2 strandedness ); NLM_EXTERN Boolean AddGapToSegmentedEntry ( NCBISubPtr submission, SeqEntryPtr segmented_seq_entry, Int4 length_of_gap ); /** 0 if not known */ NLM_EXTERN Boolean AddReferenceToSegmentedEntry ( NCBISubPtr submission , SeqEntryPtr segmented_seq_entry, CharPtr genbank_accession , Int4 gi_number , Int4 from , Int4 to , Boolean on_plus_strand ); /*** Entry contains sets of similar sequences ***/ NLM_EXTERN SeqEntryPtr AddPopSetToSubmission ( NCBISubPtr submission ); NLM_EXTERN SeqEntryPtr AddPhySetToSubmission ( NCBISubPtr submission ); NLM_EXTERN SeqEntryPtr AddMutSetToSubmission ( NCBISubPtr submission ); NLM_EXTERN SeqEntryPtr AddGenBankSetToSubmission ( NCBISubPtr submission ); /*** Entry contains nucleotide and translated proteins ***/ NLM_EXTERN SeqEntryPtr AddNucProtToSubmission ( NCBISubPtr submission ); NLM_EXTERN SeqEntryPtr AddSeqToNucProtEntry ( /** add unsegmented nuc or prot bioseq */ NCBISubPtr submission, SeqEntryPtr nuc_prot_entry, CharPtr local_name , CharPtr genbank_locus , CharPtr genbank_accession , Int4 gi_number , Int2 molecule_class, Int2 molecule_type , Int4 length , Int2 topology , Int2 strandedness ); /** add segmented nuc or prot bioseq set */ NLM_EXTERN SeqEntryPtr AddSegmentedSeqToNucProtEntry ( NCBISubPtr submission, SeqEntryPtr nuc_prot_entry , CharPtr local_name , CharPtr genbank_locus , CharPtr genbank_accession , Int4 gi_number , Int2 molecule_class, Int2 molecule_type , Int4 length , Int2 topology , Int2 strandedness ); NLM_EXTERN SeqEntryPtr AddDeltaSeqToNucProtEntry ( NCBISubPtr submission, SeqEntryPtr nuc_prot_entry , CharPtr local_name , CharPtr genbank_locus , CharPtr genbank_accession , Int4 gi_number , Int2 molecule_class, Int2 molecule_type , Int4 length , Int2 topology , Int2 strandedness ); /**** Entry contains one delta sequence ****/ NLM_EXTERN SeqEntryPtr AddDeltaSeqOnlyToSubmission ( NCBISubPtr submission, CharPtr local_name , CharPtr genbank_locus , CharPtr genbank_accession , Int4 gi_number , Int2 molecule_class, Int2 molecule_type , Int4 length , Int2 topology , Int2 strandedness ); NLM_EXTERN Boolean AddGapToDeltaSeq ( NCBISubPtr submission, SeqEntryPtr delta_seq_entry, Int4 length_of_gap ); /** 0 if not known */ NLM_EXTERN SeqLitPtr AddFakeGapToDeltaSeq ( NCBISubPtr submission, SeqEntryPtr delta_seq_entry, Int4 length_of_gap ); /** returns slp so program can set lim - unk fuzz after empty gaps are spread */ NLM_EXTERN SeqLitPtr AddLiteralToDeltaSeq ( NCBISubPtr submission, SeqEntryPtr delta_seq_entry, Int4 length_of_sequence ); #define MOLECULE_CLASS_DNA 1 #define MOLECULE_CLASS_RNA 2 #define MOLECULE_CLASS_NUC 4 #define MOLECULE_CLASS_PROTEIN 3 #define MOLECULE_TYPE_GENOMIC 1 #define MOLECULE_TYPE_PRE_MRNA 2 #define MOLECULE_TYPE_MRNA 3 #define MOLECULE_TYPE_RRNA 4 #define MOLECULE_TYPE_TRNA 5 #define MOLECULE_TYPE_SNRNA 6 #define MOLECULE_TYPE_SCRNA 7 #define MOLECULE_TYPE_PEPTIDE 8 #define MOLECULE_TYPE_OTHER_GENETIC_MATERIAL 9 #define MOLECULE_TYPE_GENOMIC_MRNA_MIX 10 #define MOLECULE_TYPE_CRNA 11 #define MOLECULE_TYPE_SNORNA 12 #define MOLECULE_TYPE_TRANSCRIBED_RNA 13 #define TOPOLOGY_LINEAR 1 #define TOPOLOGY_CIRCULAR 2 #define TOPOLOGY_TANDEM 3 #define STRANDEDNESS_SINGLE 1 #define STRANDEDNESS_DOUBLE 2 /****************************************************************** * * Fill in Bases or Amino Acids * 1) You may call functions as often per bioseq as you like * up to the length of the Bioseq * 2) All codes are iupac and defined in /ncbi/data/seqcode.prt * as an ASN.1 file used by this code. Excerpts at the * end of this file. Even though it's ASN.1 you will find * you can read it with no trouble. * 3) IUPAC codes are UPPER CASE. These functions will upper * case for you. * 4) In nucleic acids 'U' will be changed to 'T' * 5) In both cases, non-letters will be stripped from the * the input strings to facilate input from external * formatted files with numbers and internal spaces and * such. * ******************************************************************/ NLM_EXTERN Boolean AddBasesToBioseq ( NCBISubPtr submission , SeqEntryPtr the_seq , CharPtr the_bases ); NLM_EXTERN Boolean AddAminoAcidsToBioseq ( NCBISubPtr submission , SeqEntryPtr the_seq , CharPtr the_aas ); /** variant functions for Delta sequences ***/ NLM_EXTERN Boolean AddBasesToLiteral ( NCBISubPtr submission , SeqLitPtr the_literal , CharPtr the_bases ); NLM_EXTERN Boolean AddAminoAcidsToLiteral ( NCBISubPtr submission , SeqLitPtr the_literal , CharPtr the_aas ); /***************************************************************************** * * Add Annotations to Entries * *****************************************************************************/ NLM_EXTERN Boolean AddTitleToEntry ( NCBISubPtr submission, SeqEntryPtr entry , CharPtr title ); NLM_EXTERN Boolean AddSecondaryAccnToEntry ( NCBISubPtr submission, SeqEntryPtr entry , CharPtr accn ); /***************************************************************** * * rules for long comments * 1) include no non-ascii characters (e.g. \t \r \n) * 2) you may force a line feed on display by using tilde '~' * 3) you format a table by adding leading spaces after a '~' * 4) non-ascii chars will be converted on input (also for * title) \n='~', all others='#' * *****************************************************************/ NLM_EXTERN Boolean AddCommentToEntry ( NCBISubPtr submission, SeqEntryPtr entry , CharPtr comment ); NLM_EXTERN Boolean AddOrganismToEntryNew ( NCBISubPtr submission, SeqEntryPtr entry , CharPtr scientific_name , CharPtr common_name , CharPtr virus_name , CharPtr strain , CharPtr synonym1, CharPtr synonym2, CharPtr synonym3, CharPtr taxonomy ); /** AddOrganismToEntryNew() defaults to universal code (0) ** for both cytoplasmic and mitochondiral ribosomes. You ** also supply the code when you create a CdRegion. If the ** CdRegion code does not match the organism code, the ** validator will warn, but will translate by CdRegion code. ** if you need an alternate code, SetGeneticCodeForEntry() ** can be used to eliminate the conflict. See table of genetic ** codes at end of this file. You should call ** AddOrganismToEntryNew() before calling ** SetGeneticCodeForEntry() **/ NLM_EXTERN Boolean AddOrganismToEntryEx ( NCBISubPtr submission, SeqEntryPtr entry , CharPtr scientific_name , CharPtr common_name , CharPtr virus_name , CharPtr strain , CharPtr synonym1, CharPtr synonym2, CharPtr synonym3, CharPtr taxonomy, Int4 taxid ); /** AddOrganismToEntryEx() allows taxonID to be entered **/ NLM_EXTERN Boolean SetGeneticCodeForEntry ( NCBISubPtr submission, SeqEntryPtr entry, Int2 genetic_code, /* for cytoplasm */ Int2 mito_code ); /* for mitochondria */ /************************************************** * OBSOLETE!!! do not use. Use AddOrganismToEntryNew * **************************************************/ NLM_EXTERN Boolean AddOrganismToEntry ( NCBISubPtr submission, SeqEntryPtr entry , CharPtr scientific_name , CharPtr common_name , CharPtr virus_name , CharPtr strain , CharPtr synonym1, CharPtr synonym2, CharPtr synonym3); NLM_EXTERN Boolean AddGenBankBlockToEntry ( NCBISubPtr submission, SeqEntryPtr entry , CharPtr taxonomy , CharPtr division , CharPtr keyword1 , CharPtr keyword2 , CharPtr keyword3 ); #define GENOME_unknown 0 #define GENOME_genomic 1 #define GENOME_chloroplast 2 #define GENOME_chromoplast 3 #define GENOME_kinetoplast 4 #define GENOME_mitochondrion 5 #define GENOME_plastid 6 #define GENOME_macronuclear 7 #define GENOME_extrachrom 8 #define GENOME_plasmid 9 #define GENOME_transposon 10 #define GENOME_insertion_seq 11 #define GENOME_cyanelle 12 #define GENOME_proviral 13 #define GENOME_virion 14 #define GENOME_nucleomorph 15 #define GENOME_apicoplast 16 #define GENOME_leucoplast 17 #define GENOME_proplastid 18 #define GENOME_endogenous_virus 19 /******************************************** * Genome describes the type of genome from which the DNA or gene for * a protein is located. Values are: genome INTEGER { -- biological context unknown (0) , genomic (1) , chloroplast (2) , chromoplast (3) , kinetoplast (4) , mitochondrion (5) , plastid (6) , macronuclear (7) , extrachrom (8) , plasmid (9) , transposon (10) , insertion-seq (11) , cyanelle (12) , proviral (13) , virion (14) } DEFAULT unknown , more types added, see GENOME_.. above **********************************************/ NLM_EXTERN Boolean AddGenomeToEntry ( NCBISubPtr submission, SeqEntryPtr entry , Int2 type ); #define SUBSRC_chromosome 1 #define SUBSRC_map 2 #define SUBSRC_clone 3 #define SUBSRC_subclone 4 #define SUBSRC_haplotype 5 #define SUBSRC_genotype 6 #define SUBSRC_sex 7 #define SUBSRC_cell_line 8 #define SUBSRC_cell_type 9 #define SUBSRC_tissue_type 10 #define SUBSRC_clone_lib 11 #define SUBSRC_dev_stage 12 #define SUBSRC_frequency 13 #define SUBSRC_germline 14 #define SUBSRC_rearranged 15 #define SUBSRC_lab_host 16 #define SUBSRC_pop_variant 17 #define SUBSRC_tissue_lib 18 #define SUBSRC_plasmid_name 19 #define SUBSRC_transposon_name 20 #define SUBSRC_insertion_seq_name 21 #define SUBSRC_plastid_name 22 #define SUBSRC_country 23 #define SUBSRC_segment 24 #define SUBSRC_endogenous_virus_name 25 #define SUBSRC_transgenic 26 #define SUBSRC_environmental_sample 27 #define SUBSRC_isolation_source 28 #define SUBSRC_other 255 /********************************************* * SubSource defines subclasses of source material * (also see OrgMod below for subclasses of organism names) * * allowed values for type are: chromosome (1) , map (2) , clone (3) , subclone (4) , haplotype (5) , genotype (6) , sex (7) , cell-line (8) , cell-type (9) , tissue-type (10) , clone-lib (11) , dev-stage (12) , frequency (13) , germline (14) , rearranged (15) , lab-host (16) , pop-variant (17) , tissue-lib (18) , plasmid-name (19) , transposon-name (20) , insertion-seq-name (21) , plastid-name (22) , other (255) } , * value is an optional string to give the name (eg. of the * clone) ******************************************/ NLM_EXTERN Boolean AddSubSourceToEntry ( NCBISubPtr submission, SeqEntryPtr entry , Int2 type , CharPtr value); #define ORGMOD_strain 2 #define ORGMOD_substrain 3 #define ORGMOD_type 4 #define ORGMOD_subtype 5 #define ORGMOD_variety 6 #define ORGMOD_serotype 7 #define ORGMOD_serogroup 8 #define ORGMOD_serovar 9 #define ORGMOD_cultivar 10 #define ORGMOD_pathovar 11 #define ORGMOD_chemovar 12 #define ORGMOD_biovar 13 #define ORGMOD_biotype 14 #define ORGMOD_group 15 #define ORGMOD_subgroup 16 #define ORGMOD_isolate 17 #define ORGMOD_common 18 #define ORGMOD_acronym 19 #define ORGMOD_dosage 20 #define ORGMOD_nat_host 21 #define ORGMOD_sub_species 22 #define ORGMOD_specimen_voucher 23 #define ORGMOD_authority 24 #define ORGMOD_forma 25 #define ORGMOD_forma_specialis 26 #define ORGMOD_ecotype 27 #define ORGMOD_synonym 28 #define ORGMOD_anamorph 29 #define ORGMOD_teleomorph 30 #define ORGMOD_breed 31 #define ORGMOD_old_lineage 253 #define ORGMOD_old_name 254 #define ORGMOD_other 255 /********************************************* * OrgMod defines subclasses of organism names * (also see SubSource above for subclasses of source material) * * allowed values for type are: strain (2) , substrain (3) , type (4) , subtype (5) , variety (6) , serotype (7) , serogroup (8) , serovar (9) , cultivar (10) , pathovar (11) , chemovar (12) , biovar (13) , biotype (14) , group (15) , subgroup (16) , isolate (17) , common (18) , acronym (19) , dosage (20) , -- chromosome dosage of hybrid nat-host (21) , -- natural host of this specimen sub-species (22) , * value is an optional string to give the name (eg. of the * varient) ******************************************/ NLM_EXTERN Boolean AddOrgModToEntry ( NCBISubPtr submission, SeqEntryPtr entry , Int2 type , CharPtr value); /******************************************** * Biomol describes the biological type of the molecule * current values are: biomol INTEGER { unknown (0) , genomic (1) , pre-RNA (2) , -- precursor RNA of any sort really mRNA (3) , rRNA (4) , tRNA (5) , snRNA (6) , scRNA (7) , peptide (8) , other-genetic (9) , -- other genetic material genomic-mRNA (10) , -- reported a mix of genomic and cdna sequence other (255) } DEFAULT unknown , ********************************************/ NLM_EXTERN Boolean AddBiomolToEntry ( NCBISubPtr submission, SeqEntryPtr entry , Int2 type ); /******************************************** * * What technique was used to get this sequence ? * There are a set of defines in objpubd.h for this: * Current list is: #define MI_TECH_unknown 0 #define MI_TECH_standard 1 #define MI_TECH_est 2 EST division #define MI_TECH_sts 3 STS division #define MI_TECH_survey 4 GSS division #define MI_TECH_genemap 5 Bioseq is a genetic map #define MI_TECH_physmap 6 Bioseq is physical map #define MI_TECH_derived 7 Bioseq is a computed inference #define MI_TECH_concept_trans 8 conceptual translation #define MI_TECH_seq_pept 9 peptide sequencing used #define MI_TECH_both 10 combination of 8 and 9 used #define MI_TECH_seq_pept_overlap 11 peptides ordered by overlap #define MI_TECH_seq_pept_homol 12 peptides ordered by homology #define MI_TECH_concept_trans_a 13 concept trans supplied by author #define MI_TECH_other 255 doesnt' fit anything *************************************** * The following are not explicitly in the ASN.1 spec yet * but can still be legally used as numbers. * These are for High Throughput Genome Sequences * htgs_1 - preliminary data. sequence is made of multiple * contigs with gaps between them. The order of * the contigs is not known, although for * convenience they are in an arbitrary order * htgs_2 - preliminary data. like htgs_1 except the * order of the contigs is known and the sequence * reflects the correct order * htgs_3 - finished data. All annotations are machine * generated in bulk. Usually this has been placed * on a map * ****************************************** #define MI_TECH_htgs_1 14 #define MI_TECH_htgs_2 15 #define MI_TECH_htgs_3 16 **********************************************************/ NLM_EXTERN Boolean AddTechToEntry ( NCBISubPtr submission, SeqEntryPtr entry , Int2 tech ); /******************************************** * How complete is the molecule? * here are the allowed values: * completeness INTEGER { unknown (0) , complete (1) , -- complete biological entity partial (2) , -- partial but no details given no-left (3), -- KNOWN missing 5' or NH3 end no-right (4) , -- KNOWN missing 3' or COOH end no-ends (5) , -- KNOWN missing both ends has-left (6) , -- KNOWN has complete 5' or NH3 end has-right (7) , -- KNOWN has complete 3' or COOH end other (255) } DEFAULT unknown } *******************************************/ NLM_EXTERN Boolean AddCompleteToEntry ( NCBISubPtr submission, SeqEntryPtr entry , Int2 complete ); NLM_EXTERN void AddCompleteness(NCBISubPtr submission, SeqEntryPtr sep, SeqFeatPtr sfp); /**** OBSOLETE!!!! *********************************************** * DO NOT USE GIBBmethod * this is subsumed into AddTechToEntry, above * ****************************************************************/ NLM_EXTERN Boolean AddGIBBmethodToEntry ( NCBISubPtr submission, SeqEntryPtr entry , Int2 method ); #define METHOD_concept_transl 1 #define METHOD_seq_pept 2 #define METHOD_both 3 #define METHOD_seq_pept_overlap 4 #define METHOD_seq_pept_homol 5 #define METHOD_concept_transl_a 6 #define METHOD_other 255 NLM_EXTERN Boolean AddCreateDateToEntry ( NCBISubPtr submission, SeqEntryPtr entry , Int2 month , Int2 day , Int2 year ); /************************************************************************* * * Modifiers modify the meaning of all entries in the set or sequence * to which they are applied. This is particularly important for * indicating organelle sequences, RNA genomes, or mutants. * * Less obvious is indicating completness. * * A genomic sequence is assumed to be partial unless the "complete" * modifier is used. * A peptide sequence is assumed to be complete unless the "partial" * modifier is used. * A cDNA is assumed to be complete (as well as one can tell) unless * "partial" is used. * * A genomic sequence is assumed to be nuclear unless the "mitochondrial" * (or other organelle) modifier is used. * All sequences are assumed to be natural unless "synthetic", * "recombinant", or "mutagen" are used. * *************************************************************************/ /*************************************** * Adds a ValNode of the appropriate type * to the SeqEntry * Note that caller must still create the * specific descriptor structure and attach it to * the returned ValNode * ****************************************/ NLM_EXTERN ValNodePtr NewDescrOnSeqEntry (SeqEntryPtr entry, Int2 type); NLM_EXTERN ValNodePtr GetDescrOnSeqEntry ( SeqEntryPtr entry, Int2 type); NLM_EXTERN Boolean AddModifierToEntry ( NCBISubPtr submission, SeqEntryPtr entry , Int2 modifier ); #define MODIF_dna 0 #define MODIF_rna 1 #define MODIF_extrachrom 2 #define MODIF_plasmid 3 #define MODIF_mitochondrial 4 #define MODIF_chloroplast 5 #define MODIF_kinetoplast 6 #define MODIF_cyanelle 7 #define MODIF_synthetic 8 /* synthetic sequence */ #define MODIF_recombinant 9 /* recombinant construct */ #define MODIF_partial 10 #define MODIF_complete 11 #define MODIF_mutagen 12 /* subject of mutagenesis ? */ #define MODIF_natmut 13 /* natural mutant ? */ #define MODIF_transposon 14 #define MODIF_insertion_seq 15 #define MODIF_no_left 16 /* missing left end (5' for na, NH2 for aa) */ #define MODIF_no_right 17 /* missing right end (3' or COOH) */ #define MODIF_macronuclear 18 #define MODIF_proviral 19 #define MODIF_est 20 /* expressed sequence tag */ /*** add/build publications ***/ NLM_EXTERN Boolean AddPubToEntry ( NCBISubPtr submission, SeqEntryPtr entry , PubPtr pub ); NLM_EXTERN PubPtr CitSubBuild ( /* for first data submission **/ NCBISubPtr submission, Int2 month, Int2 day, Int2 year, Int2 medium ); NLM_EXTERN PubPtr CitSubUpdateBuild ( /* for updates to existing record */ NCBISubPtr submission, Int2 month, Int2 day, Int2 year , Int2 medium , CharPtr descr ); /* description of update, make it short */ #define MEDIUM_NOT_SET 0 #define MEDIUM_PAPER 1 #define MEDIUM_TAPE 2 #define MEDIUM_FLOPPY 3 #define MEDIUM_EMAIL 4 #define MEDIUM_OTHER 255 NLM_EXTERN PubPtr CitArtBuild ( NCBISubPtr submission, CharPtr title , CharPtr journal , CharPtr volume , CharPtr issue , CharPtr pages , Int2 month , Int2 day , Int2 year , Int2 status ); #define PUB_STATUS_PUBLISHED 0 #define PUB_STATUS_SUBMITTED 1 #define PUB_STATUS_IN_PRESS 2 #define PUB_STATUS_UNPUBLISHED 3 /************************************************************************* * * Author names can be given in various forms * You MUST give at least a last name * You should give at least first name or initials. * Initials are just for first and middle names, and are * separated by periods. * * example: John Q. Public * last_name = "Public" * first_name = "John" * middle_name = NULL * initials = "J.Q." * *************************************************************************/ NLM_EXTERN Boolean AddAuthorToPub ( /* call once for each author, in order */ NCBISubPtr submission, PubPtr the_pub, CharPtr last_name, CharPtr first_name, CharPtr middle_name, CharPtr initials, /* separated by periods, no initial for last name */ CharPtr suffix ); /* Jr. Sr. III */ /************************************************************************* * * Author Affiliation * only one allowed per pub (one per author is also possible, but is * not supported by this interface ) * * affil = institutional affiliation * div = division of institution * street = street address * city = city * sub = subdivision of country (e.g. state.. optional) * country = country * postal_code = zip code in the USA * *************************************************************************/ NLM_EXTERN Boolean AddAffiliationToPub ( /* call once per pub */ NCBISubPtr submission, PubPtr the_pub, CharPtr affil, /* e.g. "Xyz University" */ CharPtr div, /* e.g. "Dept of Biology" */ CharPtr street, /* e.g. "123 Academic Road" */ CharPtr city, /* e.g. "Metropolis" */ CharPtr sub, /* e.g. "Massachusetts" */ CharPtr country , /* e.g. "USA" */ CharPtr postal_code ); /* e.g."02133" */ /***************************************************************************** * * Add Features to the entry * Add location to feature * Add info for specific types to feature * *****************************************************************************/ NLM_EXTERN SeqFeatPtr FeatureBuild ( NCBISubPtr submission, SeqEntryPtr entry_to_put_feature, Boolean feature_is_partial, Uint1 evidence_is_experimental, Boolean biological_exception, CharPtr comment ); #define EVIDENCE_NOT_SET 0 #define EVIDENCE_EXPERIMENTAL 1 #define EVIDENCE_NOT_EXPERIMENTAL 2 /************************************************************************* * * About feature locations: * Internally the NCBI software represents locations on sequence as * offsets from the start of the sequence (i.e. from 0 - (length -1)). * Also, the "from" position is always <= "to", even for locations on * the minus strand. Finally, no location can cross the origin of a * circular sequence.. it must be split in two. This makes routines * that access locations very consistent and easy to write. * * However, most biologists number sequences starting with 1, not 0. * It is natural to think of a coding region on the minus strand going * from 5243 to 2993. And it is not unusual to think of the origin of * replication being from 5344 to 10 on the plus strand of a circular * sequence. * * AddIntervalToFeature and AddPointToFeature were written to support * the biological notion. They convert to the internal format * automatically. So, for these two functions: * * 1) numbers are in the range 1 - length * 2) from <= to on plus strand * to <= from on minus strand * 3) numbers not conforming to (2) are assumed to go around the origin * of a circular sequence. It is an error on a linear sequence. * 4) Intervals should be added in biological order (e.g. exon1, exon2, * exon3...) no matter which strand the feature is on. * 5) You must always indicate explicitly the Bioseq the interval is * on. You may either pass in the SeqEntryPtr or the local_name you * used when you created the sequence. The sequence must have * been previously created with AddSeqTo... If you give both the * SeqEntryPtr and the local_name, they must agree. * 6) -1 (minus one) is a short hand for "end of sequence". To indicate * the whole sequence you can give from = 1, to = -1 * *************************************************************************/ NLM_EXTERN Boolean AddIntervalToFeature ( NCBISubPtr submission, SeqFeatPtr sfp, SeqEntryPtr the_seq , CharPtr local_name , Int4 from , Int4 to , Boolean on_plus_strand , Boolean start_before_from , Boolean stop_after_to ); NLM_EXTERN Boolean AddIntToSeqFeat ( SeqFeatPtr sfp, Int4 from, Int4 to, BioseqPtr bsp, Int2 fuzz_from, Int2 fuzz_to, Int2 strand); NLM_EXTERN Boolean AddPointToFeature ( NCBISubPtr submission, SeqFeatPtr sfp, SeqEntryPtr the_seq , CharPtr local_name , Int4 location , Boolean on_plus_strand , Boolean is_after_location , Boolean is_before_location ); /************************************************************************* * * Having made a generalized feature, now add type specific info to it. * *************************************************************************/ /************************************************************ * * A comment is the simplest feature. It is required that you * supplied a "comment" argument to FeatureBuild. In GenBank format * it will appear as misc_feat, with the comment appearing as the * \note. ***************************************************************/ NLM_EXTERN Boolean MakeCommentFeature ( NCBISubPtr submission, SeqFeatPtr feature ); /***************************************************************** * * This connects a protein sequence with the nucleic acid * region which codes for it. So the protein is given as an * argument, as well as adding intervals on the nucleic acid. * A complete coding region includes the initial Met codon and * the final termination codon. * *****************************************************************/ NLM_EXTERN Boolean MakeCdRegionFeature ( NCBISubPtr submission, SeqFeatPtr feature, Int2 frame , Int2 genetic_code , /* see end of this file for genetic codes */ SeqEntryPtr protein_product, /* give id of protein. if NULL, call */ CharPtr local_id_for_protein); /* function below to create by transl */ /****************************************************************** * * A Code-break allows an exception to be made in the translation * of a particular codon. You must give positions of the first * and last bases of the codon in the DNA sequence and the amino * acid to place there, instead of the normal translation. This * should be used sparingly, and a comment on the feature should * explain why it was done. * * The location is specified the same as in AddIntervalToFeature. * AA_for_protein points the amino acid to use, in ncbieaa code. * ******************************************************************/ NLM_EXTERN Boolean AddCodeBreakToCdRegion ( NCBISubPtr submission, SeqFeatPtr sfp, SeqEntryPtr the_seq , CharPtr local_name , Int4 from , Int4 to , Boolean on_plus_strand , CharPtr AA_for_protein ); /****************************************************************** * * Special function to make protein from CdRegion feature * ******************************************************************/ NLM_EXTERN SeqEntryPtr TranslateCdRegion ( NCBISubPtr submission , SeqFeatPtr cdregion_feature , SeqEntryPtr nuc_prot_entry_to_put_sequence , CharPtr local_name , /* for protein sequence */ CharPtr genbank_locus , CharPtr genbank_accession , Int4 gi_number ); NLM_EXTERN Boolean MakeRNAFeature ( NCBISubPtr submission, SeqFeatPtr feature, Int2 rna_type , Boolean is_pseudo_gene, CharPtr rna_name , CharPtr AA_for_tRNA , CharPtr codon_for_tRNA ); #define RNA_TYPE_premsg 1 #define RNA_TYPE_mRNA 2 #define RNA_TYPE_tRNA 3 #define RNA_TYPE_rRNA 4 #define RNA_TYPE_snRNA 5 #define RNA_TYPE_scRNA 6 #define RNA_TYPE_other 255 /****************************************************************** * * Once you have made a tRNA feature, you may optionally add the * the location of the anticodon if you know it. This should be * within the range of the tRNA feature already created, obviously. * * the location is specified on the DNA the same as for * AddIntervalToFeature * ******************************************************************/ NLM_EXTERN Boolean AddAntiCodonTotRNA ( NCBISubPtr submission, SeqFeatPtr sfp, SeqEntryPtr the_seq , CharPtr local_name , Int4 from , Int4 to , Boolean on_plus_strand ); NLM_EXTERN Boolean MakeGeneFeature ( NCBISubPtr submission, SeqFeatPtr feature, CharPtr gene_symbol_for_locus , CharPtr allele , CharPtr descriptive_name , CharPtr map_location , Boolean is_pseudo_gene , CharPtr genetic_database , CharPtr gene_id_in_genetic_database , CharPtr synonym1 , CharPtr synonym2 , CharPtr synonym3 ); NLM_EXTERN Boolean MakeProteinFeature ( NCBISubPtr submission, SeqFeatPtr feature , CharPtr protein_name1, CharPtr protein_name2, CharPtr protein_name3, CharPtr descriptive_name, CharPtr ECnum1, CharPtr ECnum2, CharPtr activity1, CharPtr activity2, CharPtr protein_database, CharPtr id_in_protein_database); NLM_EXTERN Boolean MakeRegionFeature ( NCBISubPtr submission, SeqFeatPtr feature , CharPtr region_name ); NLM_EXTERN Boolean MakeSiteFeature ( NCBISubPtr submission, SeqFeatPtr feature , Int2 site_type ); NLM_EXTERN Boolean MakeImpFeature ( NCBISubPtr submission, SeqFeatPtr feature , CharPtr key ); NLM_EXTERN Boolean AddQualToImpFeature ( NCBISubPtr submission, SeqFeatPtr imp_feature , CharPtr qualifier , CharPtr value ); NLM_EXTERN Boolean MakePubFeature ( NCBISubPtr submission, SeqFeatPtr feature, PubPtr pub ); NLM_EXTERN Boolean AddBasesToByteStore (ByteStorePtr bsp, CharPtr the_bases); NLM_EXTERN Boolean AddAAsToByteStore (ByteStorePtr bsp, CharPtr the_aas); /***************************************************************************** * * AddPhrapGraph (submission, the_seq, local_name, phrap_values) * Converts phrap byte array to SeqGraph, wraps in SeqAnnot, adds to Bioseq. * The length of data in the array must be equal to the length of the Bioseq. * *****************************************************************************/ NLM_EXTERN Boolean AddPhrapGraph ( NCBISubPtr submission, SeqEntryPtr the_seq , CharPtr local_name , BytePtr phrap_values ); NLM_EXTERN Boolean AddPhrapGraphToSeqLit ( NCBISubPtr submission, SeqLitPtr slp , BytePtr phrap_values ); /* internal functions for reference gene project */ NLM_EXTERN UserObjectPtr CreateRefGeneTrackUserObject (void); NLM_EXTERN void AddStatusToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr status); NLM_EXTERN void AddCuratorToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr collaborator); NLM_EXTERN void AddAccessionToRefGeneTrackUserObject (UserObjectPtr uop, CharPtr field, CharPtr accn, Int4 gi, Boolean sequenceChange, Boolean annotationChange, CharPtr comment); /* experimental function to associate mRNA with protein product in cases of alt splicing */ NLM_EXTERN UserObjectPtr CreateMrnaProteinLinkUserObject (BioseqPtr protbsp); /* vector screen, validator count, general submission comment user object (JP) */ NLM_EXTERN UserObjectPtr CreateSubmissionUserObject (CharPtr univecComment, CharPtr additionalComment, Int4 validatorErrorCount, Int4 validatorHashCode, Boolean isCloningVector); /* clone name and ID for genomic contig RefSeq records */ NLM_EXTERN UserObjectPtr CreateContigCloneUserObject (CharPtr name, Int4 ID); /* gene ontology process, component, and function user object */ NLM_EXTERN UserObjectPtr CreateGeneOntologyUserObject ( void ); NLM_EXTERN void AddToGeneOntologyUserObject ( UserObjectPtr uop, CharPtr type, CharPtr text, Int4 goid, Int4 pmid, CharPtr evidence ); /* model evidence user object */ NLM_EXTERN UserObjectPtr CreateModelEvidenceUserObject ( CharPtr method, CharPtr contigParent ); NLM_EXTERN void AddMrnaOrESTtoModelEvidence ( UserObjectPtr uop, CharPtr type, CharPtr accn, Int4 length, Int4 gaplen ); NLM_EXTERN UserFieldPtr FindModelEvidenceField ( UserObjectPtr uop, CharPtr type ); /* third party accession list user object manipulation */ NLM_EXTERN UserObjectPtr CreateTpaAssemblyUserObject ( void ); NLM_EXTERN void AddAccessionToTpaAssemblyUserObject ( UserObjectPtr uop, CharPtr accn ); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif /***************************************************************************** * * Allowed IUPAC nucleic acid codes from /ncbi/data/seqcode.prt * ( symbol "A", name "Adenine" ), ( symbol "B" , name "G or T or C" ), ( symbol "C", name "Cytosine" ), ( symbol "D", name "G or A or T" ), ( symbol "G", name "Guanine" ), ( symbol "H", name "A or C or T" ) , ( symbol "K", name "G or T" ), ( symbol "M", name "A or C" ), ( symbol "N", name "A or G or C or T" ) , ( symbol "R", name "G or A"), ( symbol "S", name "G or C"), ( symbol "T", name "Thymine"), ( symbol "V", name "G or C or A"), ( symbol "W", name "A or T" ), ( symbol "Y", name "T or C") * * *****************************************************************************/ /***************************************************************************** * * Allowed IUPAC amino acid codes from /ncbi/data/seqcode.prt ( symbol "A", name "Alanine" ), ( symbol "B" , name "Asp or Asn" ), ( symbol "C", name "Cysteine" ), ( symbol "D", name "Aspartic Acid" ), ( symbol "E", name "Glutamic Acid" ), ( symbol "F", name "Phenylalanine" ), ( symbol "G", name "Glycine" ), ( symbol "H", name "Histidine" ) , ( symbol "I", name "Isoleucine" ), ( symbol "K", name "Lysine" ), ( symbol "L", name "Leucine" ), ( symbol "M", name "Methionine" ), ( symbol "N", name "Asparagine" ) , ( symbol "P", name "Proline" ), ( symbol "Q", name "Glutamine"), ( symbol "R", name "Arginine"), ( symbol "S", name "Serine"), ( symbol "T", name "Threoine"), ( symbol "V", name "Valine"), ( symbol "W", name "Tryptophan" ), ( symbol "X", name "Undetermined or atypical"), ( symbol "Y", name "Tyrosine"), ( symbol "Z", name "Glu or Gln" ) * * *****************************************************************************/ /***************************************************************************** * * Genetic Code id's and names from /ncbi/data/gc.prt * gc.prt lists the legal start codons and genetic codes fully * name "Standard" , id 1 , name "Vertebrate Mitochondrial" , id 2 , name "Yeast Mitochondrial" , id 3 , name "Mold Mitochondrial and Mycoplasma" , id 4 , name "Invertebrate Mitochondrial" , id 5 , name "Ciliate Macronuclear and Daycladacean" , id 6 , name "Protozoan Mitochondrial (and Kinetoplast)" , id 7 , name "Plant Mitochondrial" , id 8 , name "Echinoderm Mitochondrial" , id 9 , name "Euplotid Macronuclear" , id 10 , name "Eubacterial" , id 11 , * * *****************************************************************************/