GBrowse syn Scripts

This page describes helper scripts for processing alignment data for loading into GBrowse_syn.

Parsing Multiple Sequence Alignment Data

The scripts in this section process multiple sequence alignment data in various formats and convert them to the tab-delimited format used to load the GBRowse_syn database.

aln2hit.pl

aln2hit.pl is a generic alignment data parser that reads alignment data into the GBrowse_syn database loading format.

Purpose

Use this script in cases where you have a single alignment file and want to convert it to the tab-delimited format that is used to load the GBrowse_syn alignment database.

Example:

perl aln2hit -f clustalw -i my_alignments.aln >my_alignments.txt

Options

argument	default	description
f	clustalw	Specifies the alignment file format. MOst common formats recongnized by BioPerl's AlignIO parsers are supported. Use clustalw or fasta for best results.
i		Specifies the name of the input alignment file

clustal2hit.pl

clustal2hit.pl is a CLUSTALW format alignment data parser.

Purpose

Use this script in cases where you have a one or more clustal alignment files and want to convert them to the tab-delimited format that is used to load the GBrowse_syn alignment database.

Example:

perl clustal2hit.pl *.aln >my_alignments.txt

Options

None.

mercatoraln_to_synhits.pl

[1] is a data parser for multiple sequence alignments generated by mercator.

Purpose

This script will process alignments generated by the MERCATOR pipeline

Example:

Usage example here

Options

argument	default	description
a|aln|i|input	None	Specified the name of the alignment file
v|verbose	None	Print progress reports while running
f|format	fasta	Specifies format of the input alignment files
d|dir	None	Specifies the containing directory for the genome and map files

Direct Database Loading Scripts

The scripts in this section load data from multiple sequence alignment files into the GBrowse_syn alignment database

load_alignment_database.pl

argument	default	description

load_alignments_gff3.pl

argument	default	description

load_alignments_msa.pl

argument	default	description

split_clustal.pl

argument	default	description