--- /dev/null
+||||||||||| ReadSeq supported formats (revised 30Dec92)
+--------------------------------------------------------
+
+ -f[ormat=]Name Format name for output:
+ 1. IG/Stanford 10. Olsen (in-only)
+ 2. GenBank/GB 11. Phylip3.2
+ 3. NBRF 12. Phylip
+ 4. EMBL 13. Plain/Raw
+ 5. GCG 14. PIR/CODATA
+ 6. DNAStrider 15. MSF
+ 7. Fitch 16. ASN.1
+ 8. Pearson/Fasta 17. PAUP
+ 9. Zuker (in-only) 18. Pretty (out-only)
+
+In general, output supports only minimal subsets of each format
+needed for sequence data exchanges. Features, descriptions
+and other format-unique information is discarded.
+
+Users of Olsen multi sequence editor (VMS). The Olsen format
+here is produced with the print command:
+ print/out=some.file
+Use Genbank output from readseq to produce a format that this
+editor can read, and use the command
+ load/genbank some.file
+Dan Davison has a VMS program that will convert to/from the
+Olsen native binary data format. E-mail davison@uh.edu
+
+Warning: Phylip format input is now supported (30Dec92), however the
+auto-detection of Phylip format is very probabilistic and messy,
+especially distinguishing sequential from interleaved versions. It
+is not recommended that one use readseq to convert files from Phylip
+format to others unless essential.
+
+
+
+||||||||||| ReadSeq usage (revised 11Nov91)
+--------------------------------------------------------
+
+A. determine file format:
+
+ short skiplines; /* result: number of header lines to skip (or 0) */
+ short error; /* error result or 0 */
+ short format; /* resulting format code, see ureadseq.h */
+ char *filename = "Mysequence.file"
+
+ format = seqFileFormat( filename, &skiplines, &error);
+ if (error!=0) fail;
+
+B. read number and list of sequences (optional)
+ short numseqs; /* resulting number of sequences found in file */
+ char *seqlist; /* list of sequence names, newline separated, 0 terminated */
+
+ seqlist = listSeqs( filename, skiplines, format, &numseqs, &error);
+ if (error!=0) display (seqlist);
+ free( seqlist);
+
+C. read individual sequences as desired
+ short seqIndex; /* sequence index #, or == kListSeqs for listSeqs equivalent */
+ long seqlen; /* length of seq */
+ char seqid[256]; /* sequence name */
+ char *seq; /* sequence, 0 terminated, free when done */
+
+ seq = readSeq( seqIndex, filename, skiplines, format,
+ &seqlen, &numseqs, &error, seqid);
+ if (error!=0) manipulate(seq);
+ free(seq);
+
+D. write sequences as desired
+ int nlines; /* number of lines of sequence written */
+ FILE* fout; /* open file pointer (stdout or other) */
+ short outform; /* output format, see ureadseq.h */
+
+ nlines = writeSeq( fout, seq, seqlen, format, outform, seqid);
+
+
+Note (30Dec92): There is various processing done by the main program (in readseq.c),
+ rather than just in the subroutines (in ureadseq.c). Especially for interleaved
+ output formats, the writeSeq subroutine does not handle interleaving, nor some of
+ the formatting at the top and end of output files. While seqFileFormat, listSeqs,
+ and readSeq subroutines are fairly self-contained, the writeSeq depends a lot on
+ auxilliary processing. At some point, this may be revised so writeSeq is self-
+ contained.
+
+Note 2: The NCBI toolkit (ftp from ncbi.nlm.nih.gov) is needed for the ASN.1 format
+ reading (see ureadasn.c). A bastard (but workable I hope) ASN.1 format is written
+ by writeSeq alone.
+
+
+
+||||||||||| sequence formats....
+---------------------------------------------------
+
+stanford/IG
+;comments
+;...
+seq1 info
+abcd...
+efgh1 (or 2 = terminator)
+;another seq
+;....
+seq2 info
+abcd...1
+--- for e.g. ----
+; Dro5s-T.Seq Length: 120 April 6, 1989 21:22 Check: 9487 ..
+dro5stseq
+GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGCGGGCG
+GUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCU1
+
+; TOIG of: Dro5srna.Seq check: 9487 from: 1 to: 120
+---------------------------------------------------
+
+Genbank:
+LOCUS seq1 ID..
+...
+ORIGIN ...
+123456789abcdefg....(1st 9 columns are formatting)
+ hijkl...
+// (end of sequence)
+LOCUS seq2 ID ..
+...
+ORIGIN
+ abcd...
+//
+---------------------------------------------------
+
+NBRF format: (from uwgcg ToNBRF)
+>DL;DRO5SRNA
+Iubio$Dua0:[Gilbertd.Gcg]Dro5srna.Seq;2 => DRO5SRNA
+
+ 51 AAUUAAGCAG CGUCGCGGGC GGUUAGUACU UAGAUGGGGG ACCGCUUGGG
+ 101 AACACCGCGU GUUGUUGGCC U
+
+---------------------------------------------------
+
+EMBL format
+ID345 seq1 id (the 345 are spaces)
+... other info
+SQ345Sequence (the 3,4,5 are spaces)
+abcd...
+hijk...
+// (! this is proper end string: 12Oct90)
+ID seq2 id
+...
+SQ Sequence
+abcd...
+...
+//
+---------------------------------------------------
+
+UW GCG Format:
+comments of any form, up to ".." signal
+signal line has seq id, and " Check: #### .."
+only 1 seq/file
+
+-- e.g. --- (GCG from GenBank)
+LOCUS DROEST6 1819 bp ss-mRNA INV 31-AUG-1987
+ ... much more ...
+ORIGIN 1 bp upstream of EcoRI site; chromosome BK9 region 69A1.
+
+INVERTEBRATE:DROEST6 Length: 1819 January 9, 1989 16:48 Check: 8008 ..
+
+ 1 GAATTCGCCG GAGTGAGGAG CAACATGAAC TACGTGGGAC TGGGACTTAT
+
+ 51 CATTGTGCTG AGCTGCCTTT GGCTCGGTTC GAACGCGAGT GATACAGATG
+
+
+---------------------------------------------------
+
+DNAStrider (Mac) = modified Stanford:
+; ### from DNA Strider Friday, April 7, 1989 11:04:24 PM
+; DNA sequence pBR322 4363 b.p. complete sequence
+;
+abcd...
+efgh
+// (end of sequence)
+---------------------------------------------------
+
+Fitch format:
+Dro5srna.Seq
+ GCC AAC GAC CAU ACC ACG CUG AAU ACA UCG GUU CUC GUC CGA UCA CCG AAA UUA AGC AGC
+ GUC GCG GGC GGU UAG UAC UUA GAU GGG GGA CCG CUU GGG AAC ACC GCG UGU UGU UGG CCU
+Droest6.Seq
+ GAA TTC GCC GGA GTG AGG AGC AAC ATG AAC TAC GTG GGA CTG GGA CTT ATC ATT GTG CTG
+ AGC TGC CTT TGG CTC GGT TCG AAC GCG AGT GAT ACA GAT GAC CCT CTG TTG GTG CAG CTG
+---------------------------------------------------
+
+W.Pearson/Fasta format:
+>BOVPRL GenBank entry BOVPRL from omam file. 907 nucleotides.
+TGCTTGGCTGAGGAGCCATAGGACGAGAGCTTCCTGGTGAAGTGTGTTTCTTGAAATCAT
+
+---------------------------------------------------
+Phylip version 3.2 format (e.g., DNAML):
+
+ 5 13 YF (# seqs, #bases, YF)
+Alpha AACGTGGCCAAAT
+ aaaagggccc... (continued sp. alpha)
+Beta AAGGTCGCCAAAC
+ aaaagggccc... (continued sp. beta)
+Gamma CATTTCGTCACAA
+ aaaagggccc... (continued sp. Gamma)
+1234567890^-- bases must start in col 11, and run 'til #bases
+ (spaces & newlines are okay)
+---------------------------------------------------
+Phylip version 3.3 format (e.g., DNAML):
+
+ 5 42 YF (# seqs, #bases, YF)
+Turkey AAGCTNGGGC ATTTCAGGGT
+Salmo gairAAGCCTTGGC AGTGCAGGGT
+H. SapiensACCGGTTGGC CGTTCAGGGT
+Chimp AAACCCTTGC CGTTACGCTT
+Gorilla AAACCCTTGC CGGTACGCTT
+1234567890^-- bases must start in col 11
+ !! this version interleaves the species -- contrary to
+ all other output formats.
+
+GAGCCCGGGC AATACAGGGT AT
+GAGCCGTGGC CGGGCACGGT AT
+ACAGGTTGGC CGTTCAGGGT AA
+AAACCGAGGC CGGGACACTC AT
+AAACCATTGC CGGTACGCTT AA
+
+---------------------------------------------------
+Phylip version 3.4 format (e.g., DNAML)
+-- Both Interleaved and sequential are permitted
+
+ 5 13 (# seqs, #bases)
+Alpha AACGTGGCCAAAT
+ aaaagggccc... (continued sp. alpha)
+Beta AAGGTCGCCAAAC
+ aaaagggccc... (continued sp. beta)
+Gamma CATTTCGTCACAA
+ aaaagggccc... (continued sp. Gamma)
+1234567890^-- bases must start in col 11, and run 'til #bases
+ (spaces, newlines and numbers are are ignored)
+
+---------------------------------------------------
+Gary Olsen (multiple) sequence editor /print format:
+
+!---------------------
+!17Oct91 -- error in original copy of olsen /print format, shifted right 1 space
+! here is correct copy:
+ 301 40 Tb.thiop CGCAGCGAAA----------GCUNUGCUAAUACCGCAUA-CGnCCUG----------------------------------------------------- Tb.thiop
+123456789012345678901
+ 301 42 Rhc.purp CGUAGCGAAA----------GUUACGCUAAUACCGCAUA-UUCUGUG----------------------------------------------------- Rhc.purp
+
+ 301 44 Rhc.gela nnngnCGAAA----------GCCGGAUUAAUACCGCAUA-CGACCUA----------------------------------------------------- Rhc.gela
+!---------------------
+
+ RNase P RNA components. on 20-FEB-90 17:23:58
+
+ 1 (E.c. pr ): Base pairing in Escherichia coli RNase P RNA.
+ 2 (chrom ): Chromatium
+ :
+ 12 (B.brevis): Bacillus brevis RNase P RNA, B. James.
+ 13 ( 90% con): 90% conserved
+ 14 (100% con): 100% conserved
+ 15 (gram+ pr): pairing
+
+1
+ RNase P RNA components. on 20-FEB-90 17:23:58
+
+ Posi- Sequence
+ tion: identity: Data:
+
+ 1 1 E.c. pr <<<<<<<<<< {{{{{{{{<<:<<<<<<<<<<^<<<<<<====>>>> E.c. pr
+ 1 2 chrom GGAGUCGGCCAGACAGUCGCUUCCGUCCU------------------ chrom
+ :
+ 1 12 B.brevis AUGCAGGAAAUGCGGGUAGCCGCUGCCGCAAUCGUCU------------- B.brevis
+1234567890123456789012 <! this should be 21 not 22,
+! this example must be inset on left by 1 space from olsen /print files !
+ 1 13 90% con G C G A CGC GC - - 90% con
+ 1 14 100% con G A CGC 100% con
+ 1 15 gram+ pr <<<<<<<<<< {{{{{{{{<<<<<<<<<<<<<=============== gram+ pr
+
+ 60 1 E.c. pr >>>>>>^>>^>>>>:>> <<<^<<<< {{{{{ E.c. pr
+ 60 2 chrom -----GGUG-ACGGGGGAGGAAAGUCCGG-GCUCCAU------------- chrom
+ : :
+ 60 10 B.stearo ----UU-CG-GCCGUAGAGGAAAGUCCAUGCUCGCACGGUGCUGAGAUGC B.stearo
+
+
+---------------------------------------------------
+ GCG MSF format
+Title line
+
+picorna.msf MSF: 100 Type: P January 17, 1991 17:53 Check: 541
+..
+Name: Cb3 Len: 100 Check: 7009 Weight: 1.00
+Name: E Len: 100 Check: 60 Weight: 1.00
+
+//
+
+ 1 50
+Cb3 ...gpvedai .......t.. aaigr..vad tvgtgptnse aipaltaaet
+ E gvenae.kgv tentna.tad fvaqpvylpe .nqt...... kv.affynrs
+
+ 51 100
+
+Cb3 ghtsqvvpgd tmqtrhvkny hsrsestien flcrsacvyf teykn.....
+ E ...spi.gaf tvks...... gs.lesgfap .fsngtc.pn sviltpgpqf
+
+---------------------------------------------------
+ PIR format
+This is NBRF-PIR MAILSERVER version 1.45
+Command-> get PIR3:A31391
+\\\
+ENTRY A31391 #Type Protein
+TITLE *Esterase-6 - Fruit fly (Drosophila melanogaster)
+
+DATE 03-Aug-1992 #Sequence 03-Aug-1992 #Text 03-Aug-1992
+PLACEMENT 0.0 0.0 0.0 0.0 0.0
+COMMENT *This entry is not verified.
+SOURCE Drosophila melanogaster
+
+REFERENCE
+ #Authors Cooke P.H., Oakeshott J.G.
+ #Citation submitted to GenBank, April 1989
+ #Reference-number A31391
+ #Accession A31391
+ #Cross-reference GB:J04167
+
+SUMMARY #Molecular-weight 61125 #Length 544 #Checksum 1679
+SEQUENCE
+ 5 10 15 20 25 30
+ 1 M N Y V G L G L I I V L S C L W L G S N A S D T D D P L L V
+ 31 Q L P Q G K L R G R D N G S Y Y S Y E S I P Y A E P P T G D
+ 61 L R F E A P E P Y K Q K W S D I F D A T K T P V A C L Q W D
+ 91 Q F T P G A N K L V G E E D C L T V S V Y K P K N S K R N S
+ 121 F P V V A H I H G G A F M F G A A W Q N G H E N V M R E G K
+ 151 F I L V K I S Y R L G P L G F V S T G D R D L P G N Y G L K
+ 181 D Q R L A L K W I K Q N I A S F G G E P Q N V L L V G H S A
+ 211 G G A S V H L Q M L R E D F G Q L A R A A F S F S G N A L D
+ 241 P W V I Q K G A R G R A F E L G R N V G C E S A E D S T S L
+ 271 K K C L K S K P A S E L V T A V R K F L I F S Y V P F A P F
+ 301 S P V L E P S D A P D A I I T Q D P R D V I K S G K F G Q V
+ 331 P W A V S Y V T E D G G Y N A A L L L K E R K S G I V I D D
+ 361 L N E R W L E L A P Y L L F Y R D T K T K K D M D D Y S R K
+ 391 I K Q E Y I G N Q R F D I E S Y S E L Q R L F T D I L F K N
+ 421 S T Q E S L D L H R K Y G K S P A Y A Y V Y D N P A E K G I
+ 451 A Q V L A N R T D Y D F G T V H G D D Y F L I F E N F V R D
+ 481 V E M R P D E Q I I S R N F I N M L A D F A S S D N G S L K
+ 511 Y G E C D F K D N V G S E K F Q L L A I Y I D G C Q N R Q H
+ 541 V E F P
+///
+\\\
+---------------------------------------------------
+PAUP format:
+The NEXUS Format
+
+Every block starts with "BEGIN blockname;" and ends with "END;".
+Each block is composed of one or more statements, each
+terminated by a semicolon (;).
+
+Comments may be included in NEXUS files by enclosing them within
+square brackets, as in "[This is a comment]."
+
+NEXUS-conforming files are identified by a "#NEXUS" directive at
+the very beginning of the file (line 1, column 1). If the
+#NEXUS is omitted PAUP issues a warning but continues
+processing.
+
+NEXUS files are entirely free-format. Blanks, tabs, and
+newlines may be placed anywhere in the file. Unless RESPECTCASE
+is requested, commands and data may be entered in upper case,
+lower case, or a mixture of upper and lower case.
+
+The following conventions are used in the syntax descriptions of
+the various blocks. Upper-case items are entered exactly as
+shown. Lower-case items inside of angle brackets -- e.g., <x>
+-- represent items to be substituted by the user. Items inside
+of square brackets -- e.g., [X] -- are optional. Items inside
+of curly braces and separated by vertical bars -- e.g., { X | Y
+| Z } -- are mutually exclusive options.
+
+
+The DATA Block
+
+The DATA block contains the data matrix and other associated
+information. Its syntax is:
+
+BEGIN DATA;
+DIMENSIONS NTAX=<number of taxa> NCHAR=<number of characters>;
+ [ FORMAT [ MISSING=<missing-symbol> ]
+ [ LABELPOS={ LEFT | RIGHT } ]
+ [ SYMBOLS="<symbols-list>" ]
+ [ INTERLEAVE ]
+ [ MATCHCHAR=<match-symbol> ]
+ [ EQUATE="<symbol>=<expansion> [<symbol>=<expansion>...]" ]
+ [ TRANSPOSE ]
+ [ RESPECTCASE ]
+ [ DATATYPE = { STANDARD | DNA | RNA | PROTEIN } ]; ]
+ [ OPTIONS [ IGNORE={ INVAR | UNINFORM } ]
+ [ MSTAXA = { UNCERTAIN | POLYMORPH | VARIABLE } ]
+ [ ZAP = "<list of zapped characters>" ] ; ]
+ [ CHARLABELS <label_1> label_2>ÊÉ <label_NCHAR> ; ]
+ [ TAXLABELS <label1_1> <label1_2> <label1_NTAX> ; ]
+ [ STATELABELS <currently ignored by PAUP> ; ]
+ MATRIX <data-matrix> ;
+ END;
+
+--- example PAUP file
+
+#NEXUS
+
+[!Brown et al. (1982) primate mitochondrial DNA]
+
+begin data;
+ dimensions ntax=5 nchar=896;
+ format datatype=dna matchchar=. interleave missing='-';
+ matrix
+[ 2 4 6 8 ]
+[ 1 1 1 1 1 ]
+human aagcttcaccggcgcagtca ttctcataatcgcccacggR cttacatcctcattactatt ctgcctagcaaactcaaact acgaacgcactcacagtcgc
+chimp ................a.t. .c.................a ...............t.... ..................t. .t........c.........
+gorilla ..................tg ....t.....t........a ........a......t.... .................... .......a..c.....c...
+orang ................ac.. cc.....g..t.....t..a ..c........cc....g.. .................... .......a..c.....c...
+gibbon ......t..a..t...ac.g .c.................a ..a..c..t..cc.g..... ......t............. .......a........c...
+
+[ 8 8 8 8 8 8 ]
+[ 0 2 4 6 8 9 ]
+[ 1 1 1 1 1 6 ]
+human cttccccacaacaatattca tgtgcctagaccaagaagtt attatctcgaactgacactg agccacaacccaaacaaccc agctctccctaagctt
+chimp t................... .a................c. ........a.....g..... ...a................ ................
+gorilla ..................tc .a................c. ........a.g......... ...a.............tt. .a..............
+orang ta....a...........t. .c.......ga......acc ..cg..a.a......tg... .a.a..c.....g...cta. .a.....a........
+gibbon a..t.......t........ ....ac...........acc .....t..a........... .a.tg..........gctag .a..............
+ ;
+end;
+---------------------------------------------------
+
+
+
+
+
+
+||||||||||| Sample SMTP mail header
+---------------------------------------------------
+
+- - - - - - - - -
+From GenBank-Retrieval-System@genbank.bio.net Sun Nov 10 17:28:56 1991
+Received: from genbank.bio.net by sunflower.bio.indiana.edu
+ (4.1/9.5jsm) id AA19328; Sun, 10 Nov 91 17:28:55 EST
+Received: by genbank.bio.net (5.65/IG-2.0)
+ id AA14458; Sun, 10 Nov 91 14:30:03 -0800
+Date: Sun, 10 Nov 91 14:30:03 -0800
+Message-Id: <9111102230.AA14458@genbank.bio.net>
+From: Database Server <GenBank-Retrieval-System@genbank.bio.net>
+To: gilbertd@sunflower.bio.indiana.edu
+Subject: Results of Query for drorna
+Status: R
+
+No matches on drorna.
+- - - - - -
+From GenBank-Retrieval-System@genbank.bio.net Sun Nov 10 17:28:49 1991
+Received: from genbank.bio.net by sunflower.bio.indiana.edu
+ (4.1/9.5jsm) id AA19323; Sun, 10 Nov 91 17:28:47 EST
+Received: by genbank.bio.net (5.65/IG-2.0)
+ id AA14461; Sun, 10 Nov 91 14:30:03 -0800
+Date: Sun, 10 Nov 91 14:30:03 -0800
+Message-Id: <9111102230.AA14461@genbank.bio.net>
+From: Database Server <GenBank-Retrieval-System@genbank.bio.net>
+To: gilbertd@sunflower.bio.indiana.edu
+Subject: Results of Query for droest6
+Status: R
+
+LOCUS DROEST6 1819 bp ss-mRNA INV 31-AUG-1987
+DEFINITION D.melanogaster esterase-6 mRNA, complete cds.
+ACCESSION M15961
+
+
+
+
+
+
+
+
+
+
+
+
+||||||||||| GCG manual discussion of sequence symbols:
+---------------------------------------------------
+
+III_SEQUENCE_SYMBOLS
+
+
+ GCG programs allow all upper and lower case letters, periods (.),
+asterisks (*), pluses (+), ampersands (&), and ats (@) as symbols in
+biological sequences. Nucleotide symbols, their complements, and the
+standard one-letter amino acid symbols are shown below in separate lists.
+The meanings of the symbols +, &, and @ have not been assigned at this
+writing (March, 1989).
+
+ GCG uses the letter codes for amino acid codes and nucleotide
+ambiguity proposed by IUB (Nomenclature Committee, 1985,
+Eur. J. Biochem. 150; 1-5). These codes are compatible with the codes
+used by the EMBL, GenBank, and NBRF data libraries.
+
+
+ NUCLEOTIDES
+
+ The meaning of each symbol, its complement, and the Cambridge and
+Stanford equivalents are shown below. Cambridge files can be converted
+into GCG files and vice versa with the programs FROMSTADEN and TOSTADEN.
+IntelliGenetics sequence files can be interconverted with the programs
+FROMIG and TOIG.
+
+IUB/GCG Meaning Complement Staden/Sanger Stanford
+
+ A A T A A
+ C C G C C
+ G G C G G
+ T/U T A T T/U
+ M A or C K 5 J
+ R A or G Y R R
+ W A or T W 7 L
+ S C or G S 8 M
+ Y C or T R Y Y
+ K G or T M 6 K
+ V A or C or G B not supported N
+ H A or C or T D not supported N
+ D A or G or T H not supported N
+ B C or G or T V not supported N
+ X/N G or A or T or C X -/X N
+ . not G or A or T or C . not supported ?
+
+
+ The frame ambiguity codes used by Staden are not supported by GCG
+and are translated by FROMSTADEN as the lower case single base
+equivalent.
+
+ Staden Code Meaning GCG
+
+ D C or CC c
+ V T or TT t
+ B A or AA a
+ H G or GG g
+ K C or CX c
+ L T or TX t
+ M A or AX a
+ N G or GX g
+
+
+ AMINO ACIDS
+
+ Here is a list of the standard one-letter amino acid codes and their
+three-letter equivalents. The synonymous codons and their depiction in
+the IUB codes are shown. You should recognize that the codons following
+semicolons (;) are not sufficiently specific to define a single amino
+acid even though they represent the best possible back translation into
+the IUB codes! All of the relationships in this list can be redefined by
+the user in a local data file described below.
+
+ IUB
+Symbol 3-letter Meaning Codons Depiction
+ A Ala Alanine GCT,GCC,GCA,GCG !GCX
+ B Asp,Asn Aspartic,
+ Asparagine GAT,GAC,AAT,AAC !RAY
+ C Cys Cysteine TGT,TGC !TGY
+ D Asp Aspartic GAT,GAC !GAY
+ E Glu Glutamic GAA,GAG !GAR
+ F Phe Phenylalanine TTT,TTC !TTY
+ G Gly Glycine GGT,GGC,GGA,GGG !GGX
+ H His Histidine CAT,CAC !CAY
+ I Ile Isoleucine ATT,ATC,ATA !ATH
+ K Lys Lysine AAA,AAG !AAR
+ L Leu Leucine TTG,TTA,CTT,CTC,CTA,CTG
+!TTR,CTX,YTR;YTX
+ M Met Methionine ATG !ATG
+ N Asn Asparagine AAT,AAC !AAY
+ P Pro Proline CCT,CCC,CCA,CCG !CCX
+ Q Gln Glutamine CAA,CAG !CAR
+ R Arg Arginine CGT,CGC,CGA,CGG,AGA,AGG
+!CGX,AGR,MGR;MGX
+ S Ser Serine TCT,TCC,TCA,TCG,AGT,AGC !TCX,AGY;WSX
+ T Thr Threonine ACT,ACC,ACA,ACG !ACX
+ V Val Valine GTT,GTC,GTA,GTG !GTX
+ W Trp Tryptophan TGG !TGG
+ X Xxx Unknown !XXX
+ Y Tyr Tyrosine TAT, TAC !TAY
+ Z Glu,Gln Glutamic,
+ Glutamine GAA,GAG,CAA,CAG !SAR
+ * End Terminator TAA, TAG, TGA !TAR,TRA;TRR
+
+
+
+
+
+
+
+
+||||||||||| docs from PSC on sequence formats:
+---------------------------------------------------
+
+
+ Nucleic Acid and Protein Sequence File Formats
+
+
+It will probably save you some time if you have your data in a usable
+format before you send it to us. However, we do have the University of
+Wisconsin Genetics Computing Group programs running on our VAXen and
+this package includes several reformatting utilities. Our programs
+usually recognize any of several standard formats, including GenBank,
+EMBL, NBRF, and MolGen/Stanford. For the purposes of annotating an
+analysis we find the GenBank and EMBL formats most useful, particularly
+if you have already received an accession number from one of these
+organizations for your sequence.
+
+Our programs do not require that all of the line types available in
+GenBank, EMBL, or NBRF file formats be present for the file format to
+be recognized and processed. The following pages outline the essential
+details required for correct processing of files by our programs.
+Additional information may be present but will generally be ignored.
+
+
+ GenBank File Format
+
+File Header
+
+1. The first line in the file must have "GENETIC SEQUENCE DATA BANK"
+ in spaces 20 through 46 (see LINE 1, below).
+2. The next 8 lines may contain arbitrary text. They are ignored but
+ are required to maintain the GenBank format (see LINE 2 - LINE 9).
+
+Sequence Data Entries
+
+3. Each sequence entry in the file should have the following format.
+ a) first line: Must have LOCUS in the first 5 spaces. The
+ genetic locus name or identifier must be in spaces
+ 13 - 22. The length of the sequences is right
+ justified in spaces 23 through 29 (see LINE 10).
+ b) second line: Must have DEFINITION in the first 10 spaces.
+ Spaces 13 - 80 are free form text to identify the
+ sequence (see LINE 11).
+ c) third line: Must have ACCESSION in the first 9 spaces. Spaces
+ 13 - 18 must hold the primary accession number
+ (see LINE 12).
+ d) fourth line: Must have ORIGIN in the first 6 spaces. Nothing
+ else is required on this line, it indicates that
+ the nucleic acid sequence begins on the next line
+ (see LINE 13).
+ e) fifth line: Begins the nucleotide sequence. The first 9
+ spaces of each sequence line may either be blank
+ or may contain the position in the sequence of the
+ first nucleotide on the line. The next 66 spaces
+ hold the nucleotide sequence in six blocks of ten
+ nucleotides. Each of the six blocks begins with a
+ blank space followed by ten nucleotides. Thus the
+ first nucleotide is in space eleven of the line while
+ the last is in space 75 (see LINE 14, LINE 15).
+ f) last line: Must have // in the first 2 spaces to indicate
+ termination of the sequence (see LINE 16).
+
+NOTE: Multiple sequences may appear in each file. To begin another
+ sequence go back to a) and start again.
+
+
+ Example GenBank file
+
+
+LINE 1 : GENETIC SEQUENCE DATA BANK
+LINE 2 :
+LINE 3 :
+LINE 4 :
+LINE 5 :
+LINE 6 :
+LINE 7 :
+LINE 8 :
+LINE 9 :
+LINE 10 :LOCUS L_Name Length BP
+LINE 11 :DEFINITION Describe the sequence any way you want
+LINE 12 :ACCESSION Accession Number
+LINE 13 :ORIGIN
+LINE 14 : 1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt a...
+LINE 15 : 61 acgt...
+LINE 16 ://
+
+
+
+ EMBL File Format
+
+Unlike the GenBank file format the EMBL file format does not require
+a series of header lines. Thus the first line in the file begins
+the first sequence entry of the file.
+
+1. The first line of each sequence entry contains the two letters ID
+ in the first two spaces. This is followed by the EMBL identifier
+ in spaces 6 through 14. (See LINE 1).
+
+2. The second line of each sequence entry has the two letters AC in
+ the first two spaces. This is followed by the accession number in
+ spaces 6 through 11. (See LINE 2).
+
+3. The third line of each sequence entry has the two letters DE in the
+ first two spaces. This is followed by a free form text definition
+ in spaces 6 through 72. (See LINE 3).
+
+4. The fourth line in each sequence entry has the two letters SQ in
+ the first two spaces. This is followed by the length of the
+ sequence beginning at or after space 13. After the sequence length
+ there is a blank space and the two letters BP. (See LINE 4).
+
+5. The nucleotide sequence begins on the fifth line of the sequence
+ entry. Each line of sequence begins with four blank spaces. The
+ next 66 spaces hold the nucleotide sequence in six blocks of ten
+ nucleotides. Each of the six blocks begins with a blank space
+ followed by ten nucleotides. Thus the first nucleotide is in space
+ 6 of the line while the last is in space 70. (See LINE 5 -
+ LINE 6).
+
+6. The last line of each sequence entry in the file is a terminator
+ line which has the two characters // in the first two spaces.
+ (See LINE 7).
+
+7. Multiple sequences may appear in each file. To begin another
+ sequence go back to item 1 and start again.
+
+
+ Example EMBL file
+
+LINE 1 :ID ID_name
+LINE 2 :AC Accession number
+LINE 3 :DE Describe the sequence any way you want
+LINE 4 :SQ Length BP
+LINE 5 : ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTA...
+LINE 6 : ACGT...
+LINE 7 ://
+
+
+
+ NBRF (protein or nucleic acid) File Format
+
+1. The first line of each sequence entry begins with a greater than
+ symbol, >. This is immediately followed by the two character
+ sequence type specifier. Space four must contain a semi-colon.
+ Beginning in space five is the sequence name or identification code
+ for the NBRF database. The code is from four to six letters and
+ numbers. (See LINE 1).
+
+!!!! >> add these to readseq
+ Specifier Sequence type
+
+ P1 protein, complete
+ F1 protein, fragment
+ DL DNA, linear
+ DC DNA, circular
+ RL RNA, linear
+ RC RNA, circular
+ N1 functional RNA, other than tRNA
+ N3 tRNA
+
+2. The second line of each sequence entry contains two kinds of
+ information. First is the sequence name which is separated from
+ the organism or organelle name by the three character sequence
+ blank space, dash, blank space, " - ". There is no special
+ character marking the beginning of this line. (See LINE 2).
+
+3. Either the amino acid or nucleic acid sequence begins on line three
+ and can begin in any space, including the first. The sequence is
+ free format and may be interrupted by blanks for ease of reading.
+ Protein sequences man contain special punctuation to indicate
+ various indeterminacies in the sequence. In the NBRF data files
+ all lines may be up to 500 characters long. However some PSC
+ programs currently have a limit of 130 characters per line
+ (including blanks), and BitNet will not accept lines of over eighty
+ characters. (See LINE 3, LINE 4, and LINE 5).
+
+ The last character in the sequence must be an asterisks, *.
+
+ Example NBRF file
+
+ LINE 1 :>P1;CBRT
+ LINE 2 :Cytochrome b - Rat mitochondrion (SGC1)
+ LINE 3 :M T N I R K S H P L F K I I N H S F I D L P A P S
+ LINE 4 : VTHICRDVN Y GWL IRY
+ LINE 5 :TWIGGQPVEHPFIIIGQLASISYFSIILILMPISGIVEDKMLKWN*
+
+
+
+ MolGen/Stanford File Format
+
+1. The first line in a sequence file is a comment line. This line
+ begins with a semi-colon in the first space. This line need
+ not be present. If it is present it holds descriptive text.
+ There may be as many comment lines as desired at the first of
+ sequence file. (See LINE 1).
+
+2. The second line must be present and contains an identifier or
+ name for the sequence in the first ten spaces. (See LINE 2).
+
+3. The sequence begins on the third line and occupies up to eighty
+ spaces. Spaces may be included in the sequence for ease of
+ reading. The sequence continues for as many line as needed
+ and is terminated with a 1 or 2. 1 indicates a linear sequence
+ while 2 marks a circular sequence. (See LINE 3 and LINE 4).
+
+ Example MolGen/Stanford file
+
+LINE 1 :; Describe the sequence any way you want
+LINE 2 :ECTRNAGLY2
+LINE 3 :ACGCACGTAC ACGTACGTAC A C G T C C G T ACG TAC GTA CGT
+LINE 4 : GCTTA GG G C T A1
+
+
+
+
+||||||||||| Phylip file format
+---------------------------------------------------
+
+ Phylip 3.3 File Format (DNA sequences)
+
+
+ The input and output formats for PROTPARS and for RESTML are described in
+their document files. In general their input formats are similar to those
+described here, except that the one-letter codes for data are specific to those
+programs and are described in those document files. Since the input formats
+for the eight DNA sequence programs apply to all eight, they are described
+here. Their input formats are standard: the data have A's, G's, C's and T's
+(or U's). The first line of the input file contains the number of species and
+the number of sites. As with the other programs, options information may
+follow this. In the case of DNAML, DNAMLK, and DNADIST an additional line
+(described in the document file for these pograms) may follow the first one.
+Following this, each species starts on a new line. The first 10 characters of
+that line are the species name. There then follows the base sequence of that
+species, each character being one of the letters A, B, C, D, G, H, K, M, N, O,
+R, S, T, U, V, W, X, Y, ?, or - (a period was also previously allowed but it is
+no longer allowed, because it sometimes is used to in aligned sequences to mean
+"the same as the sequence above"). Blanks will be ignored, and so will
+numerical digits. This allows GENBANK and EMBL sequence entries to be read
+with minimum editing.
+
+ These characters can be either upper or lower case. The algorithms
+convert all input characters to upper case (which is how they are treated).
+The characters constitute the IUPAC (IUB) nucleic acid code plus some slight
+extensions. They enable input of nucleic acid sequences taking full account of
+any ambiguities in the sequence.
+
+The sequences can continue over multiple lines; when this is done the sequences
+must be either in "interleaved" format, similar to the output of alignment
+programs, or "sequential" format. These are described in the main document
+file. In sequential format all of one sequence is given, possibly on multiple
+lines, before the next starts. In interleaved format the first part of the
+file should contain the first part of each of the sequences, then possibly a
+line containing nothing but a carriage-return character, then the second part
+of each sequence, and so on. Only the first parts of the sequences should be
+preceded by names. Here is a hypothetical example of interleaved format:
+
+ 5 42
+Turkey AAGCTNGGGC ATTTCAGGGT
+Salmo gairAAGCCTTGGC AGTGCAGGGT
+H. SapiensACCGGTTGGC CGTTCAGGGT
+Chimp AAACCCTTGC CGTTACGCTT
+Gorilla AAACCCTTGC CGGTACGCTT
+
+GAGCCCGGGC AATACAGGGT AT
+GAGCCGTGGC CGGGCACGGT AT
+ACAGGTTGGC CGTTCAGGGT AA
+AAACCGAGGC CGGGACACTC AT
+AAACCATTGC CGGTACGCTT AA
+
+while in sequential format the same sequences would be:
+
+ 5 42
+Turkey AAGCTNGGGC ATTTCAGGGT
+GAGCCCGGGC AATACAGGGT AT
+Salmo gairAAGCCTTGGC AGTGCAGGGT
+GAGCCGTGGC CGGGCACGGT AT
+H. SapiensACCGGTTGGC CGTTCAGGGT
+ACAGGTTGGC CGTTCAGGGT AA
+Chimp AAACCCTTGC CGTTACGCTT
+AAACCGAGGC CGGGACACTC AT
+Gorilla AAACCCTTGC CGGTACGCTT
+AAACCATTGC CGGTACGCTT AA
+
+
+Note, of course, that a portion of a sequence like this:
+
+ 300 AAGCGTGAAC GTTGTACTAA TRCAG
+
+is perfectly legal, assuming that the species name has gone before, and is
+filled out to full length by blanks. The above digits and blanks will be
+ignored, the sequence being taken as starting at the first base symbol (in this
+case an A).
+
+ The present versions of the programs may sometimes have difficulties with
+the blank lines between groups of lines, and if so you might want to retype
+those lines, making sure that they have only a carriage-return and no blank
+characters on them, or you may perhaps have to eliminate them. The symptoms of
+this problem are that the programs complain that the sequences are not properly
+aligned, and you can find no other cause for this complaint.
+
+------------------------------------------------
+
+
+||||||||||| ASN.1 file format
+---------------------------------------------------
+
+
+ASN.1 -- see NCBI toolkit docs, source and examples (ncbi.nlm.nih.gov)
+
+Example asn.1 sequence file----
+
+Bioseq-set ::= {
+seq-set {
+ seq {
+ id { local id 1 } , -- id essential
+ descr { title "Dummy sequence data from nowhere" } , -- optional
+ inst { -- inst essential
+ repr raw ,
+ mol dna ,
+ length 156 ,
+ topology linear ,
+ seq-data
+ iupacna "GAATTCATTTTTGAAACAAATCGACCTGACGACGGAATGGTACTCGAATTA
+TGGGCCAAAGGGTTTTATGGGACAAATTAATAGGTGTTCATTATATGCCACTTTCGGAGATTAGATACAGCAATGCAG
+TGGATTCAAAGCAATAGAGTTGTTCTT"
+ } } ,
+
+ seq {
+ id { local id 2 } ,
+ descr { title "Dummy sequence 2 data from somewhere else" } ,
+ inst {
+ repr raw ,
+ mol dna ,
+ length 150 ,
+ topology linear ,
+ seq-data
+ iupacna "TTTTTTTTTTTTGAAACAAATCGACCTGACGACGGAATGGTACTCGAATTA
+TGGGCCAAAGGGTTTTATGGGACAAATTAATAGGTGTTCATTATATGCCACTTTCGGAGATTAGATACAGCAATGCAG
+TGGATTCAAAGCAATAGAGTT"
+ }
+ }
+ }
+ }
+
+
+partial ASN.1 description from toolkit
+
+Bioseq ::= SEQUENCE {
+ id SET OF Seq-id , -- equivalent identifiers
+ descr Seq-descr OPTIONAL , -- descriptors
+ inst Seq-inst , -- the sequence data
+ annot SET OF Seq-annot OPTIONAL }
+
+Seq-inst ::= SEQUENCE { -- the sequence data itself
+ repr ENUMERATED { -- representation class
+ not-set (0) , -- empty
+ virtual (1) , -- no seq data
+ raw (2) , -- continuous sequence
+ seg (3) , -- segmented sequence
+ const (4) , -- constructed sequence
+ ref (5) , -- reference to another sequence
+ consen (6) , -- consensus sequence or pattern
+ map (7) , -- ordered map (genetic, restriction)
+ other (255) } ,
+ mol ENUMERATED { -- molecule class in living organism
+ not-set (0) , -- > cdna = rna
+ dna (1) ,
+ rna (2) ,
+ aa (3) ,
+ na (4) , -- just a nucleic acid
+ other (255) } ,
+ length INTEGER OPTIONAL , -- length of sequence in residues
+ fuzz Int-fuzz OPTIONAL , -- length uncertainty
+ topology ENUMERATED { -- topology of molecule
+ not-set (0) ,
+ linear (1) ,
+ circular (2) ,
+ tandem (3) , -- some part of tandem repeat
+ other (255) } DEFAULT linear ,
+ strand ENUMERATED { -- strandedness in living organism
+ not-set (0) ,
+ ss (1) , -- single strand
+ ds (2) , -- double strand
+ mixed (3) ,
+ other (255) } OPTIONAL , -- default ds for DNA, ss for RNA, pept
+ seq-data Seq-data OPTIONAL , -- the sequence
+ ext Seq-ext OPTIONAL , -- extensions for special types
+ hist Seq-hist OPTIONAL } -- sequence history
+
+------------------------------------------------
git://source.jalview.org / jpred.git / blobdiff