seqret.txt

emboss的linux版本的源代码

Output file format

   The output from seqret is one or more sequences, and by default will
   be written in FASTA format.

   If the '-firstonly' qualifier is used then only the first sequence of
   the input USA specification will be written out.

   In some cases the output filename will be the same as the input
   filename, but as seqret reads only the first sequence before opening
   the output file it may try to overwrite the input. Note that this is
   not true of seqretset which reads all sequences into memory at
   startup, but which can need a large amount of memory for many
   sequences.

  Output files for usage example

  File: hsfau.fasta

>HSFAU X65923.1 H.sapiens fau mRNA
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa

  Output files for usage example 2

  File: hsall.seq

>HS989235 H45989.1 yo13c02.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA cl
one IMAGE:177794 3', mRNA sequence.
ccggnaagctcancttggaccaccgactctcgantgnntcgccgcgggagccggntggan
aacctgagcgggactggnagaaggagcagagggaggcagcacccggcgtgacggnagtgt
gtggggcactcaggccttccgcagtgtcatctgccacacggaaggcacggccacgggcag
gggggtctatgatcttctgcatgcccagctggcatggccccacgtagagtggnntggcgt
ctcggtgctggtcagcgacacgttgtcctggctgggcaggtccagctcccggaggacctg
gggcttcagcttcccgtagcgctggctgcagtgacggatgctcttgcgctgccatttctg
ggtgctgtcactgtccttgctcactccaaaccagttcggcggtccccctgcggatggtct
gtgttgatggacgtttgggctttgcagcaccggccgccgagttcatggtngggtnaagag
atttgggttttttcn
>HSCAD5 X59796.1 H.sapiens mRNA for cadherin-5
ctccactcacgctcagccctggacggacaggcagtccaacggaacagaaacatccctcag
cccacaggcacgatctgttcctcctgggaagatgcagaggctcatgatgctcctcgccac
atcgggcgcctgcctgggcctgctggcagtggcagcagtggcagcagcaggtgctaaccc
tgcccaacgggacacccacagcctgctgcccacccaccggcgccaaaagagagattggat
ttggaaccagatgcacattgatgaagagaaaaacacctcacttccccatcatgtaggcaa
gatcaagtcaagcgtgagtcgcaagaatgccaagtacctgctcaaaggagaatatgtggg
caaggtcttccgggtcgatgcagagacaggagacgtgttcgccattgagaggctggaccg
ggagaatatctcagagtaccacctcactgctgtcattgtggacaaggacactggcgaaaa
cctggagactccttccagcttcaccatcaaagttcatgacgtgaacgacaactggcctgt
gttcacgcatcggttgttcaatgcgtccgtgcctgagtcgtcggctgtggggacctcagt
catctctgtgacagcagtggatgcagacgaccccactgtgggagaccacgcctctgtcat
gtaccaaatcctgaaggggaaagagtattttgccatcgataattctggacgtattatcac
aataacgaaaagcttggaccgagagaagcaggccaggtatgagatcgtggtggaagcgcg
agatgcccagggcctccggggggactcgggcacggccaccgtgctggtcactctgcaaga
catcaatgacaacttccccttcttcacccagaccaagtacacatttgtcgtgcctgaaga
cacccgtgtgggcacctctgtgggctctctgtttgttgaggacccagatgagccccagaa
ccggatgaccaagtacagcatcttgcggggcgactaccaggacgctttcaccattgagac
aaaccccgcccacaacgagggcatcatcaagcccatgaagcctctggattatgaatacat
ccagcaatacagcttcatagtcgaggccacagaccccaccatcgacctccgatacatgag
ccctcccgcgggaaacagagcccaggtcattatcaacatcacagatgtggacgagccccc
cattttccagcagcctttctaccacttccagctgaaggaaaaccagaagaagcctctgat
tggcacagtgctggccatggaccctgatgcggctaggcatagcattggatactccatccg
caggaccagtgacaagggccagttcttccgagtcacaaaaaagggggacatttacaatga
gaaagaactggacagagaagtctacccctggtataacctgactgtggaggccaaagaact
ggattccactggaacccccacaggaaaagaatccattgtgcaagtccacattgaagtttt
ggatgagaatgacaatgccccggagtttgccaagccctaccagcccaaagtgtgtgagaa
cgctgtccatggccagctggtcctgcagatctccgcaatagacaaggacataacaccacg
aaacgtgaagttcaaattcatcttgaatactgagaacaactttaccctcacggataatca
cgataacacggccaacatcacagtcaagtatgggcagtttgaccgggagcataccaaggt
ccacttcctacccgtggtcatctcagacaatgggatgccaagtcgcacgggcaccagcac
gctgaccgtggccgtgtgcaagtgcaacgagcagggcgagttcaccttctgcgaggatat
ggccgcccaggtgggcgtgagcatccaggcagtggtagccatcttactctgcatcctcac
catcacagtgatcaccctgctcatcttcctgcggcggcggctccggaagcaggcccgcgc
gcacggcaagagcgtgccggagatccacgagcagctggtcacctacgacgaggagggcgg
cggcgagatggacaccaccagctacgatgtgtcggtgctcaactcggtgcgccgcggcgg
ggccaagcccccgcggcccgcgctggacgcccggccttccctctatgcgcaggtgcagaa
gccaccgaggcacgcgcctggggcacacggagggcccggggagatggcagccatgatcga
ggtgaagaaggacgaggcggaccacgacggcgacggccccccctacgacacgctgcacat
ctacggctacgagggctccgagtccatagccgagtccctcagctccctgggcaccgactc


  [Part of this file has been deleted for brevity]

aacaaaaaaagagaatgttacaccaatatccttgatgaacatcgatgcaaaaatcctcaa
taaaatactggcaaactgaatccagcagcacatcaaaaagcttatcctccatgatcaagt
gggcttcatccctgccatgcaaggctggttcaacatacgaaatcaataaacataatccag
catataaacagaaccaaagacacaaaccatatgattatctcaatagatgcagaaaaggcc
tttgacaaaattcaacaatgcttcatgctaaaaactctcaataaattaggtattgatggg
acatatctcaaaataataagagctatctatgacaaacccacagccaatatcatactgagt
ggacaaaaactggaagcattccctttgaaaactggcacaaggcagggatgccctctctca
ccactcctattcaacatagtgttggaagttctggccagggcaatcaggcaggagaaggaa
ataaagggcattcaattaggaaaagaggaaggtgaaattgtccctgtttgcagatgacat
gattgtatatctagaaaaccccattgtctcagcccaaaatctccttaagctgataagcaa
cttcagcaaagtctcaggatataaaatcagtgtgcaaaaatcacaagtattcctatgcac
caataacagacaaacagagagccaaatcatgagtgaactcccattcacaattgcttcaaa
gagaataaaatacctaggaatccaacttacaagggatgtgaaggacctcttcaaggagaa
ctacaaaccactgctcaatgaaataaaagaggatacaaacaaatggaagaacattccatg
cttatgggtaggaagaatcatatcgtgaaaatggtcatactgcccaaggtaatttataga
ttcaatgccatccccatcaagctaccaatgactttcttcacagaactggaaaaaactact
ttaaagttcatatggaatcaaaaaagagcccacatcaccaaggcaatcctaagccaaaag
aacaaagctggaggcatcacgctacctgacttcaaactatactacaatgctacggtaacc
aaaacagcatggtactggtaccaaaacagagatctagaccaatggaacagaacagagccc
tcagaaataatgccgcatatctacaactatccgatctttgacaaacctgagagaaacaag
caatggggaaaggattccctatttaataaatggtgctgggaaaactggctagccatatgt
agaaagctgaaactggatccttccttacaccttatacaaaaattaattcaagatggatta
aagacttaaacattagacctaaaaccataaaaaccctagaaaaaaacctaggcaatacca
ttcaggacataggcatgggcaaggacttcatgtctaaaacaccaaaacgaatggcaacaa
aagacaaaatggacaaacgggatctaattaaactaaagagcttctgcacagctaaagaaa
ctaccatcagagtgaacaggcaacctacaaaatgggagaaaatttttgcaatctactcat
ctgacaaagggctaatatccagaatctacaatgaactcaaacaaatttacaagaaaaaac
aaacaaccccatcaaaaagtgggcaaaggatatgaacagacacttctcaaaagaagacat
ttatgtaatcaaaaaacacatgaaaaaatgctcatcatcactagccatcagagaaatgca
aatcaaaaccacaatgagataccatctcacaccagttagaatggcgatcattaaaaagtc
aggaaacaacaggtgctggagaggatgtggagaaacaggaacaacttttacactgttggt
gggactgtaaactagttcaaccattgcggaagtcagtgtggcaattcctcaggaatctag
aactagaaataccatttgacccagccatcccattactgggtagatacccaaaggattata
aatcatgctgctataaagacacatgcacacgtatgtttattgcagcactattcacaatag
caaagacttggaaccaacccaaatgtccaacaacgatagattggattaagaaaatgtggc
acatatacaccatggaatactatgcagccataaaaaatgatgagttcatgtcctttgtag
ggacatggatgaagctggaaactatcattctcagcaaactatcacaaggacaataaacca
aacaccgcatgttctcactcataggtgggaattgaacaatgagaacacatggacacatga
agaggaacatcacactctggggactgttatggggtggggggcaggggcagggatagcact
aggagatatacctaatgctaaatgacgagttaatgggtgcagcacaccaacatggcacat
gtatacatatataacaaacctgccgttgtgcacatgtaccctaaaacttgaagtataata
ataaaaaaaagttatcctattaaaactgatctcacacatccgtagagccattatcaagtc
tttctctttgaaacagacagaaatttagtgttttctcagtcagttaac
>HSA203YC1 Z52466.1 H.sapiens (D1S2660) DNA segment containing (CA) repeat; clo
ne AFMa203yc1; single read.
agctgtgtgcacacaacatganggggcacacatgcacatgcacacatgcccacatgcata
tgcacacacacacacacacacacacacacattcatgcccaagcacgcccaccctcatgtc
tcaccatgtgcacataacacacagtcacatataccctggcacacatgcccacatgcagac
acgaaacacaggcccacgnttncatgcacacaggtatgggcacacataccatgcacacat
aangacaaataccaggccagacatgatttgcccctgctggtgtcactgttaagtgtgaca
gacaagcagaggacacacacccacctgggacgcggggcttcaggagagaggcagacctaa
tagggcccggattcggggctggggaggct

  Output files for usage example 3

  File: hsfau.embl

ID   HSFAU      standard; DNA; UNC; 518 BP.
AC   X65923;
SV   X65923.1
DE   H.sapiens fau mRNA
KW   fau gene.
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /chromosome="11q"
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /tissue_type="placenta"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /map="13"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /db_xref="SWISS-PROT:P35544"
FT                   /db_xref="SWISS-PROT:Q05472"
FT                   /gene="fau"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLA
G
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKT
G
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        6
0
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       12
0
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       18
0
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       24
0
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       30
0
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       36
0
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       42
0
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       48
0
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               51
8
//

  Output files for usage example 5

  File: hsfau.gcg

!!NA_SEQUENCE 1.0

H.sapiens fau mRNA

HSFAU  Length: 518  Type: N  Check: 2981 ..

   1 ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc

  51 gccaatatgc agctctttgt ccgcgcccag gagctacaca ccttcgaggt

 101 gaccggccag gaaacggtcg cccagatcaa ggctcatgta gcctcactgg

 151 agggcattgc cccggaagat caagtcgtgc tcctggcagg cgcgcccctg

 201 gaggatgagg ccactctggg ccagtgcggg gtggaggccc tgactaccct

 251 ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc

 301 gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag

 351 aagaagaaga agacaggtcg ggctaagcgg cggatgcagt acaaccggcg

 401 ctttgtcaac gttgtgccca cctttggcaa gaagaagggc cccaatgcca

 451 actcttaagt cttttgtaat tctggctttc tctaataaaa aagccactta

 501 gttcagtcaa aaaaaaaa

  Output files for usage example 8

  File: hsfau.fasta

>HSFAU X65923.1 H.sapiens fau mRNA
ttttttttttgactgaactaagtggcttttttattagagaaagccagaattacaaaagac
ttaagagttggcattggggcccttcttcttgccaaaggtgggcacaacgttgacaaagcg
ccggttgtactgcatccgccgcttagcccgacctgtcttcttcttcttcttctcctgttt
ggccaccttaggagtctgacctctcacttttccagcacgggccagggaaccatgaacttt
acctccaagcatgcggcctgctacttccagggtagtcagggcctccaccccgcactggcc
cagagtggcctcatcctccaggggcgcgcctgccaggagcacgacttgatcttccggggc
aatgccctccagtgaggctacatgagccttgatctgggcgaccgtttcctggccggtcac
ctcgaaggtgtgtagctcctgggcgcggacaaagagctgcatattggcgactgaacggcg
gtcccagctaccgcgaagatggagtcgagaaagaggaa

  Output files for usage example 9

  File: hsfau.fasta

>HSFAU X65923.1 H.sapiens fau mRNA
tctttctcgactccatcttcg

  Output files for usage example 10

  File: hsfau.fasta

>HSFAU X65923.1 H.sapiens fau mRNA
tctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcagct
ctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgccca
gatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcct
ggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgac
taccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggcccgtgc
tggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaagaagac
aggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgcccacctt
tggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttctcta
ataaaaaagccacttagttcagtcaaaaaa

Data files

   None.

Notes

   This description of what you can do when reading or writing files is
   not specific to the program seqret. All EMBOSS programs that read or
   write sequences can do the same.

   seqret is often one of the first programs taught in EMBOSS training
   courses. This is because it is versatile, it is extremely powerful for
   its size (17 lines of code) it illustrates many aspects of EMBOSS
   programs and it was one of the first EMBOSS programs to be written, so
   it has a special place in the hearts of EMBOSS developers.

   The name 'seqret' derives both from its function ("sequence return")
   and from the fact that immense amounts of functionality can come from
   so few lines of source code - most of the work is done by the EMBOSS
   libraries which the program calls and whose complexity is hidden, or
   "secret".

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name                         Description
   biosed       Replace or delete sequence sections
   codcopy      Reads and writes a codon usage table
   cutseq       Removes a specified section from a sequence
   degapseq     Removes gap characters from sequences
   descseq      Alter the name or description of a sequence
   entret       Reads and writes (returns) flatfile entries
   extractalign Extract regions from a sequence alignment
   extractfeat  Extract features from a sequence
   extractseq   Extract regions from a sequence
   listor       Write a list file of the logical OR of two sets of sequences
   makenucseq   Creates random nucleotide sequences
   makeprotseq  Creates random protein sequences
   maskfeat     Mask off features of a sequence
   maskseq      Mask off regions of a sequence
   newseq       Type in a short new sequence
   noreturn     Removes carriage return from ASCII files
   notseq       Exclude a set of sequences and write out the remaining ones
   nthseq       Writes one sequence from a multiple set of sequences
   pasteseq     Insert one sequence into another
   revseq       Reverse and complement a sequence
   seqretsplit  Reads and writes (returns) sequences in individual files
   skipseq      Reads and writes (returns) sequences, skipping first few
   splitter     Split a sequence into (overlapping) smaller sequences
   trimest      Trim poly-A tails off EST sequences
   trimseq      Trim ambiguous bits off the ends of sequences
   union        Reads sequence fragments and builds one sequence
   vectorstrip  Strips out DNA between a pair of vector sequences
   yank         Reads a sequence range, appends the full USA to a list file

   Valid names of the databases set up in your local implementation of
   EMBOSS can be seen by using the program 'showdb'.

Author(s)

   Peter Rice (pmr