revseq.txt

emboss的linux版本的源代码

                                  revseq 



Function

   Reverse and complement a sequence

Description

   This takes a sequence and outputs the reverse complement (also known
   as the anti-sense or reverse sense) sequence.

   It can also output just the reversed sequence or just the complement
   of the sequence.

Usage

   Here is a sample session with revseq

   To create the reverse complement (reverse sense) of 'tembl:hsfau' in
   the file 'hsfau.rev':


% revseq tembl:hsfau hsfau.rev 
Reverse and complement a sequence

   Go to the input files for this example
   Go to the output files for this example

   Example 2

   To create the complement of 'tembl:hsfau' in the file 'hsfau.rev':


% revseq tembl:hsfau hsfau.rev -norev 
Reverse and complement a sequence

   Go to the output files for this example

   Example 3

   To create the reverse of 'tembl:hsfau' in the file 'hsfau.rev':


% revseq tembl:hsfau hsfau.rev -nocomp 
Reverse and complement a sequence

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) nucleotide sequence(s) filename and
                                  optional format, or reference (input USA)
  [-outseq]            seqoutall  [.] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -[no]reverse        boolean    [Y] Set this to be false if you do not wish
                                  to reverse the output sequence
   -[no]complement     boolean    [Y] Set this to be false if you do not wish
                                  to complement the output sequence

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   revseq reads one or more nucleic acid sequence USAs.

  Input files for usage example

   'tembl:hsfau' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:hsfau

ID   HSFAU      standard; RNA; HUM; 518 BP.
XX
AC   X65923;
XX
SV   X65923.1
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   23-SEP-1993 (Rel. 37, Last updated, Version 10)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-518
RX   MEDLINE; 93368957.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8:2537-2546(1993).
XX
DR   SWISS-PROT; P35544; UBIM_HUMAN.
DR   SWISS-PROT; Q05472; RS30_HUMAN.
XX
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
XX
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 file format

   One or more sequences are written out.

  Output files for usage example

  File: hsfau.rev

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

  Output files for usage example 2

  File: hsfau.rev

>HSFAU X65923.1 H.sapiens fau mRNA
aaggagaaagagctgaggtagaagcgccatcgaccctggcggcaagtcagcggttatacg
tcgagaaacaggcgcgggtcctcgatgtgtggaagctccactggccggtcctttgccagc
gggtctagttccgagtacatcggagtgacctcccgtaacggggccttctagttcagcacg
aggaccgtccgcgcggggacctcctactccggtgagacccggtcacgccccacctccggg
actgatgggaccttcatcgtccggcgtacgaacctccatttcaagtaccaagggaccggg
cacgaccttttcactctccagtctgaggattccaccggtttgtcctcttcttcttcttct
tctgtccagcccgattcgccgcctacgtcatgttggccgcgaaacagttgcaacacgggt
ggaaaccgttcttcttcccggggttacggttgagaattcagaaaacattaagaccgaaag
agattattttttcggtgaatcaagtcagtttttttttt

  Output files for usage example 3

  File: hsfau.rev

>HSFAU X65923.1 H.sapiens fau mRNA
aaaaaaaaaactgacttgattcaccgaaaaaataatctctttcggtcttaatgttttctg
aattctcaaccgtaaccccgggaagaagaacggtttccacccgtgttgcaactgtttcgc
ggccaacatgacgtaggcggcgaatcgggctggacagaagaagaagaagaagaggacaaa
ccggtggaatcctcagactggagagtgaaaaggtcgtgcccggtcccttggtacttgaaa
tggaggttcgtacgccggacgatgaaggtcccatcagtcccggaggtggggcgtgaccgg
gtctcaccggagtaggaggtccccgcgcggacggtcctcgtgctgaactagaaggccccg
ttacgggaggtcactccgatgtactcggaactagacccgctggcaaaggaccggccagtg
gagcttccacacatcgaggacccgcgcctgtttctcgacgtataaccgctgacttgccgc
cagggtcgatggcgcttctacctcagctctttctcctt

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   Bugs noted but not yet fixed.

   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
   seqret       Reads and writes (returns) sequences
   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

Author(s)

   Gary Williams (gwilliam