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     Sequence database USA
  [-outseq]            seqoutall  Output sequence(s) USA

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


Standard (Mandatory) qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence database USA Readable sequence(s) Required
[-outseq]
(Parameter 2)
Output sequence(s) USA Writeable sequence(s) <sequence>.format
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-[no]reverse Set this to be false if you do not wish to reverse the output sequence Boolean value Yes/No Yes
-[no]complement Set this to be false if you do not wish to complement the output sequence Boolean value Yes/No Yes

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="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
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        60
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
//

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 nameDescription
biosedReplace or delete sequence sections
codcopyReads and writes a codon usage table
cutseqRemoves a specified section from a sequence
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
listorWrite a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
notseqExclude a set of sequences and write out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
skipseqReads and writes (returns) sequences, skipping first few
splitterSplit a sequence into (overlapping) smaller sequences
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
yankReads a sequence range, appends the full USA to a list file

Author(s)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Completed 26 Jan 1999

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None