cat_seq

cat_seq

A script to merge multi-sequence RichSeq files into one single-entry 'artificial' sequence file.

Synopsis

perl cat_seq.pl multi-seq_file.embl

Description

This script concatenates multiple sequences in a RichSeq file (embl or genbank, but also fasta) to a single artificial sequence. The first sequence in the file is used as a foundation to add the subsequent sequences, along with all features and annotations.

Optionally, a different output file format can be specified (fasta/embl/genbank).

Usage

Merge multi-sequence file

perl cat_seq.pl multi-seq_file.gbk

Merge multi-sequence file and specify different output format

perl cat_seq.pl multi-seq_file.embl [fasta|genbank]

UNIX loop to concatenate each multi-sequence file in the current working directory

for i in *.[embl|fasta|gbk]; do perl cat_seq.pl $i [embl|fasta|genbank]; done

Concatenate multi-sequence fasta files faster with UNIXs grep

If you're working only with fasta files UNIXs grep is a faster choice to concatenate sequences.

grep -v ">" seq.fasta > seq_artificial.fasta

Subsequently add as a first line a fasta ID (starting with '>') with an editor.

Output

• *_artificial.[embl|fasta|genbank]

Concatenated artificial sequence in the input format, or optionally the specified output sequence format.

Run environment

The Perl script runs under Windows and UNIX flavors.

Dependencies (not in the core Perl modules)

• BioPerl (tested with version 1.006901)

Alternative software

The EMBOSS (The European Molecular Biology Open Software Suite) application union can also be used for this task (http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/union.html).

Author/contact

Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)

Changelog

• v0.1 (08.02.2013)