Dendrome Project

TreeGenes::Scripts

Here are a few resources available to facilitate bioinformatic needs. All of the scripts here are written in Perl and require libraries that have been installed on our system. These utilities assist with parsing, processing, and sequence comparisons. To select the entire script, simply double click on any section of the code. If you encounter difficulties with any of the scripts listed here or would like to submit your own, please contact the help desk.

Script Name	Description
addcolumn.pl	This script adds a column to a column file specified by an arithmetic string
blast_summary_tophits.pl	This script will parse a blastx or blastn result and has two output formats that summarize the blast output, see below for example, both outputs ignore Queries with no hits
getcolumns.pl	This script extracts a column from a multicolumn file (splits on whitespace by default). You can specify more than one column at a time by - or -
grepseq.pl	Extract sub-sequences from sequences on stdin based on a (perl) regular expression given on the cmd line. Input sequences in labeled fasta format. By default the labels are searched using the regexp.
gseq.pl	batchextract retrieves one or more sequence entries from NCBI specified by accession numbers. These must be given either as standard input, as seperate arguments or from a file.
histogram.pl	Makes a 2D or 3D histogram data-set for gnuplot from data in specified column(s) of an input file. Lines not starting with a real number are ignored. It also understands ``framed'' tables dumped from databases.
mmaquery.pl	mrnaquery.pl retrieves the accession numbers of all the mRNA sequences for a specified organism from Genbank, omitting ESTs, STSs, working drafts and patents. If the optional third argument is not given, the output is written to STDOUT
nuclcount.pl	This script counts n-mers in a set of sequences.
orfprune.pl	Prunes a seqfile of open reading frames. Either by masking of removing sequence entries
pickseq.pl	Picks out sequence entries from a sequence file based on id/accession. It takes a newline separated list of ids/accessions to pick, either as first argument or from STDIN. Genbank and EMBL entries is identified by their accession. Fasta by id
reformat.pl	This script does reformatting between sequence formats. It handles GenBank, EMBL, Fasta and all the other formats supported by bioperl. In addition it formats to labeled fasta (lfa) which is the a handy extention of the fasta format
seqfilediff.pl	Reports the differences between two sequence files, and prints either the sequences unique to file1 or the sequences that the files have in common
splitbyorg.pl	This script splits EMBL/GenBank/Swissprot entries in a file/stream into subfiles for each organism
subseq.pl	Outputs specified subsequence from fasta file
tablefilter.pl	This script filters a table based on a specifies string of conditions. Quote the string in '' not to interpolate the $ vars in the shell.
tablesort.pl	Specify what columns to sort by. Default is to sort from column one and onwards until the row is unique
wu_tblastn_parser.php	WU-TBLASTN output parser
PineSAP.pl	PineSAP script

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