||||||||||| 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 >>>>>^>>^>>>>:>> <<<^<<<< {{{{{ 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., -- 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= NCHAR=; [ FORMAT [ MISSING= ] [ LABELPOS={ LEFT | RIGHT } ] [ SYMBOLS="" ] [ INTERLEAVE ] [ MATCHCHAR= ] [ EQUATE="= [=...]" ] [ TRANSPOSE ] [ RESPECTCASE ] [ DATATYPE = { STANDARD | DNA | RNA | PROTEIN } ]; ] [ OPTIONS [ IGNORE={ INVAR | UNINFORM } ] [ MSTAXA = { UNCERTAIN | POLYMORPH | VARIABLE } ] [ ZAP = "" ] ; ] [ CHARLABELS label_2>�� ; ] [ TAXLABELS ; ] [ STATELABELS ; ] 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 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 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 ------------------------------------------------