NAME

ReverseComplement.pl - Computes the reverse complement for each sequence in a given multiple fasta file

SYNOPSIS

 # Minimal argument call, specifying all required parameters.
 ReverseComplement.pl --input fastafile.fa --output reversecomplement.fa
 
 # Maximal argument call, specifying all possible parameters.
 ReverseComplement.pl --input fastafile.fa --output reversecomplement.fa --append "_rc"

OPTIONS

--input

The input file. Has to be a multiple fasta file. Mandatory parameter

--output

The output file. Mandatory parameter

--append

A short string which should be appended to the ID of each reverse complemented nucleotide sequence. This is to distinguish the reverse complement sequences from the original ones. default="_rc"

--help

Display the help pages

DESCRIPTION

General

The script calculates the reverse complement for each nucleotide sequence in a specified input file. A small string may be appended to each nucleotide sequence as to distinguish the reverse complement sequences from the original ones.

Input

Multiple fasta files. For example:

 >cel-let-7 MI0000001 Caenorhabditis elegans let-7 stem-loop
 TACACTGTGGATCCGGTGAGGTAGTAGGTTGTATAGTTTGGAATATTACC
 ACCGGTGAACTATGCAATTTTCTACCTTACCGGAGACAGAACTCTTCGA
 >cel-lin-4 MI0000002 Caenorhabditis elegans lin-4 stem-loop
 ATGCTTCCGGCCTGTTCCCTGAGACCTCAAGTGTGAGTGTACTATTGATG
 CTTCACACCTGGGCTCTCCGGGTACCAGGACGGTTTGAGCAGAT
 >cel-mir-1 MI0000003 Caenorhabditis elegans miR-1 stem-loop
 AAAGTGACCGTACCGAGCTGCATACTTCCTTACATGCCCATACTATATCA
 TAAATGGATATGGAATGTAAAGAAGTATGTAGAACGGGGTGGTAGT
 >cel-mir-2 MI0000004 Caenorhabditis elegans miR-2 stem-loop
 TAAACAGTATACAGAAAGCCATCAAAGCGGTGGTTGATGTGTTGCAAATT
 ATGACTTTCATATCACAGCCAGCTTTGATGTGCTGCCTGTTGCACTGT
 >cel-mir-34 MI0000005 Caenorhabditis elegans miR-34 stem-loop
 CGGACAATGCTCGAGAGGCAGTGTGGTTAGCTGGTTGCATATTTCCTTGA
 CAACGGCTACCTTCACTGCCACCCCGAACATGTCGTCCATCTTTGAA

Output

A multiple fasta file, containing the reverse complement of each sequence. A small string (--append) may be appended to each fasta-ID (default="_rc"); For example:

 >cel-let-7 MI0000001 Caenorhabditis elegans let-7 stem-loop_rc
 TCGAAGAGTTCTGTCTCCGGTAAGGTAGAAAATTGCATAGTTCACCGGTG
 GTAATATTCCAAACTATACAACCTACTACCTCACCGGATCCACAGTGTA
 >cel-lin-4 MI0000002 Caenorhabditis elegans lin-4 stem-loop_rc
 ATCTGCTCAAACCGTCCTGGTACCCGGAGAGCCCAGGTGTGAAGCATCAA
 TAGTACACTCACACTTGAGGTCTCAGGGAACAGGCCGGAAGCAT
 >cel-mir-1 MI0000003 Caenorhabditis elegans miR-1 stem-loop_rc
 ACTACCACCCCGTTCTACATACTTCTTTACATTCCATATCCATTTATGAT
 ATAGTATGGGCATGTAAGGAAGTATGCAGCTCGGTACGGTCACTTT
 >cel-mir-2 MI0000004 Caenorhabditis elegans miR-2 stem-loop_rc
 ACAGTGCAACAGGCAGCACATCAAAGCTGGCTGTGATATGAAAGTCATAA
 TTTGCAACACATCAACCACCGCTTTGATGGCTTTCTGTATACTGTTTA
 >cel-mir-34 MI0000005 Caenorhabditis elegans miR-34 stem-loop_rc
 TTCAAAGATGGACGACATGTTCGGGGTGGCAGTGAAGGTAGCCGTTGTCA
 AGGAAATATGCAACCAGCTAACCACACTGCCTCTCGAGCATTGTCCG

REQUIREMENTS

Perl 5.8 or higher

AUTHORS

Robert Kofler

Heinz Himmelbauer

CONTACT

robert.kofler at crg.es