![]() ![]() ME, 5 MINUTES LATER: This time I want to search a different file (bzip2-compressed) for 3 sequences and their reverse complements. ME AGAIN: Oops, I forgot to search for the sequence's reverse complement as well. I'll use grep.ĪLSO ME: Oh, the file is gzip-compressed. ME: I just need to search for a sequence in this text file real quick. There are circumstances in which this extra work is justified, but many times you just need a flexible tool to do a quick-n-dirty search.Ĭonsider the following, totally not-real never-happened-to-me hypothetical situation. If input files are compressed in a certain way, or stored in a non-standard format, there is usually some non-trivial work and storage involved in converting the data to a format the software will accept. RA Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.There are many wonderfully elegant and efficient tools for performing all sorts of exact and inexact searches on large collections of DNA sequences.Įxperience has shown, however, that these tools are usually very rigid with respect to their assumptions about input data. Michiels, University of Antwerp, Dept of Biochemistry, RL Submitted (2) to the EMBL/GenBank/DDBJ databases. OC Eutheria Euarchontoglires Primates Haplorrhini Catarrhini Hominidae OC Eukaryota Metazoa Chordata Craniata Vertebrata Euteleostomi Mammalia ID X65923 SV 1 linear mRNA STD HUM 518 BP. 'tembl:圆5923' is a sequence entry in the example nucleic acid database 'tembl' (nbrf), swissprot (swiss, sw), dasgff and debug.įor further information on sequence formats. Gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir The input format can be specified by using theĬommand-line qualifier -sformat xxx, where 'xxx' is replacedīy the name of the required format. Written by an EMBOSS or third-party application. Installations include srs:embl, srs:uniprot and ensemblĭata can also be read from sequence output in any supported format Major sequence database sources defined as standard in EMBOSS ![]() The input is a standard EMBOSS sequence query (also known as a 'USA'). Revseq reads one or more nucleotide sequences. More information on associated and general qualifiers can be found with -help -verbose Prompt for standard and additional values Read first file from standard input, write first file to standard output "-outseq" associated seqoutall qualifiers Set this to be false if you do not wish to complement the output sequence Set this to be false if you do not wish to reverse the output sequence Sequence set(s) filename and optional format (output USA) (Gapped) nucleotide sequence(s) filename and optional format, or reference (input USA) version boolean Report version number and exit die boolean Report dying program messages Qualifiers can be found with -help -verbose help boolean Report command line options and exit. verbose boolean Report some/full command line options debug boolean Write debug output to program.dbg options boolean Prompt for standard and additional values filter boolean Read first file from standard input, write stdout boolean Write first file to standard output ossingle2 boolean Separate file for each entry snucleotide1 boolean Sequence is nucleotide send1 integer End of each sequence to be used sbegin1 integer Start of each sequence to be used complement boolean Set this to be false if you do not wish reverse boolean Set this to be false if you do not wish seqoutall Sequence set(s)įilename and optional format (output USA) Optional format, or reference (input USA) seqall (Gapped) nucleotide sequence(s) filename and To create the reverse of 'tembl:圆5923' in the file '圆5923.rev': To create the complement of 'tembl:圆5923' in the file '圆5923.rev': To create the reverse complement (reverse sense) of 'tembl:圆5923' in the file '圆5923.rev': It can also output just the reversed sequence or just the complement of the sequence. Revseq reads one or more nucleotide sequences and writes to file the reverse complement (also known as the anti-sense or reverse sense) of each sequence. Reverse and complement a nucleotide sequence Please help by correcting and extending the Wiki pages. The master copies of EMBOSS documentation are available ![]()
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