A developer of mine has this requirement - I couldn't tell her quickly how to do it with UNIX commands or a quick script so she's writing a quick program to do it - but that got my curiousity up and thought I'd ask here for advice.
In a text file, there are some records (about half of them)... (4 Replies)
Hi.. I have a seperate chromosome sequences and i wanted to parse some regions of chromosome based on start site and end site.. how can i achieve this?
For Example Chr 1 is in following format
I need regions from 2 - 10 should give me AATTCCAAA
and in a similar way 15- 25 should give... (8 Replies)
Hi all !
I have a fasta file that looks like that:
>Sequence1
RTYIPLCASQHKLCPITFLAVK
(it's just an example, obviously in reality I have several pairs of lines like that)
Using UNIX command(s), would it be possible to replace all the characters except the "C" of the second line only by... (7 Replies)
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
I have fasta files with multiple sequences in each. I need to change the sequence name headers from:
>accD:_59176-60699
ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA
>atpA_(reverse_strand):_showing_revcomp_of_10525-12048
ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC... (2 Replies)
I need assistance with following requirement, I am new to Unix.
I want to do the following task but stuck with file creation date(sysdate)
Following is the requirement
I need to create a script that will read the abc/xyz/klm folder and look for *.err files for that day’s date and then send an... (4 Replies)
Hi,
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
input
> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
> fefrwefrwef X937... (2 Replies)
Hello,
I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)
Hi
This is my first post and I'm just a beginner. So please be nice to me.
I have a couple of html files where a pattern beginning with "http://www.site.com" and ending with "/resource.dat" is present on every 241st line. How do I extract this to a new text file?
I have tried sed -n 241,241p... (13 Replies)
Discussion started by: dejavo
13 Replies
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tfbs::patterngen::elph
TFBS::PatternGen::Elph(3pm) User Contributed Perl Documentation TFBS::PatternGen::Elph(3pm)NAME
TFBS::PatternGen::Elph - a pattern factory that uses the Elph program
SYNOPSIS
my $patterngen =
TFBS::PatternGen::Elph->new(-seq_file=>'sequences.fa',
-binary => '/Elph/elph'
-motif_length => [8, 9, 10],
-additional_params => '-x -r -e');
my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
DESCRIPTION
TFBS::PatternGen::Gibbs builds position frequency matrices using an advanced Gibbs sampling algorithm implemented in external Gibbs program
by Chip Lawrence. The algorithm can produce multiple patterns from a single set of sequences.
new
Title : new
Usage : my $db = TFBS::PatternGen::Gibbs->new(%args);
Function: the constructor for the TFBS::PatternGen::Gibbs object
Returns : a TFBS::PatternGen::Gibbs object
Args : This method takes named arguments;
you must specify one of the following three
-seq_list # a reference to an array of strings
# and/or Bio::Seq objects
# or
-seq_stream # A Bio::SeqIO object
# or
-seq_file # the name of the fasta file containing
# all the sequences
Other arguments are:
-binary # a fully qualified path to Gibbs executable
# OPTIONAL: default 'Gibbs'
-nr_hits # a presumed number of pattern occurences in the
# sequence set: it can be a single integer, e.g.
# -nr_hits => 24 , or a reference to an array of
# integers, e.g -nr_hits => [12, 24, 36]
-motif_length # an expected length of motif in nucleotides:
# it can be a single integer, e.g.
# -motif_length => 8 , or a reference to an
# array ofintegers, e.g -motif_length => [8..12]
-additional_params # a string containing additional
# command-line switches for the
# Gibbs program
pattern
all_patterns
patternSet
The three methods listed above are used for the retrieval of patterns, and are common to all TFBS::PatternGen::* classes. Please see
TFBS::PatternGen for details.
perl v5.14.2 2008-01-24 TFBS::PatternGen::Elph(3pm)