I am trying to write a bash script that would be able to read DNA sequences (each line in the file is a sequence) from a file, where sequences are separated by an empty line. I am then to find the amino acid that these DNA sequences encode per codon (each group of three literals.) For example, if I have a file with the sequence:
then starting from GCA (first three literals,) I want to decode the DNA into amino acids based on the following table:
that is, I need to get:
Then I need to print the name of each Amino Acid and how many times it was used. For example:
and so on. I have 100s of files with DNA sequences in them, but I am not that good at bash. I tried awk and tr but I did not know how to code the table into a bash script.
Last edited by faizlo; 10-08-2015 at 09:08 PM..
Reason: Add CODE tags.
Hi all,
I have a requirement where the variable name starts with $, like
$Amd=/home/student/test/
How to work wit it? can some one help me, am in gr8 confusion:confused: (5 Replies)
Hi all,
Using Perl, I need to extract DNA bases from a GenBank file for a given plant species. A sample GenBank file is here...
Nucleotide
This is saved on my computer as NC_001666.gb. I also have a file that is saved on my computer as NC_001666.txt. This text file has a list of all... (5 Replies)
I am trying to reverse and complement my DNA sequences. The file format is FASTA, something like this:
Now, to reverse the sequence, I should start reading from right to left. At the same should be complemented. Thus, "A" should be read as "T"; "C" should be read as "G"; "T" should be converted... (8 Replies)
Hi all,
I have a file like this
ID 3BP5L_HUMAN Reviewed; 393 AA.
AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 05-SEP-2012, entry version 71.
FT COILED 59 140 ... (1 Reply)
Looking for a simple way to convert ranges to a numerical sequence that would assign the original value of the range to the individual numbers that are on the range.
Thank you
given data
13196-13199 0
13200 4
13201 10
13202-13207 3
13208-13210 7
desired... (3 Replies)
Hi,
I am having a file of dna sequences in fasta format which look like this:
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat
with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
If I run rm -rf * command under one parent directory.
/data > rm -rf *
Is there anyway to know which files will be deleted first ?
Start using code tags please, ty. (2 Replies)
Discussion started by: sameermohite
2 Replies
LEARN ABOUT DEBIAN
bio::tools::analysis::dna::esefinder
Bio::Tools::Analysis::DNA::ESEfinder(3pm) User Contributed Perl Documentation Bio::Tools::Analysis::DNA::ESEfinder(3pm)NAME
Bio::Tools::Analysis::DNA::ESEfinder - a wrapper around ESEfinder server
SYNOPSIS
use Bio::Tools::Analysis::DNA::ESEfinder;
use strict;
my $seq; # a Bio::PrimarySeqI or Bio::SeqI object
$seq = Bio::Seq->new(
-primary_id => 'test',
-seq=>'atgcatgctaggtgtgtgttttgtgggttgtactagctagtgat'.
-alphabet=>'dna');
my $ese_finder = Bio::Tools::Analysis::DNA::ESEfinder->
new(-seq => $seq);
# run ESEfinder prediction on a DNA sequence
$ese_finder->run();
die "Could not get a result"
unless $ese_finder->status =~ /^COMPLETED/;
print $ese_finder->result; # print raw prediction to STDOUT
foreach my $feat ( $ese_finder->result('Bio::SeqFeatureI') ) {
# do something to SeqFeature
# e.g. print as GFF
print $feat->gff_string, "
";
# or store within the sequence - if it is a Bio::SeqI
$seq->add_SeqFeature($feat)
}
DESCRIPTION
This class is a wrapper around the ESEfinder web server which uses experimentally defined scoring matrices to identify possible exonic
splicing enhancers in human transcripts.
The results can be retrieved in 4 ways.
1. "$ese_finder->result('')" retrieves the raw text output of the program
2. "$ese_finder->result('all')" returns a Bio::Seq::Meta::Array object with prediction scores for all residues in the sequence
3. "$ese_finder->result('Bio::SeqFeatureI')" returns an array of Bio::SeqFeature objects for sequences with significant scores. Feature
tags are score, motif, SR_protein and method
4. "$ese_finder->result('raw')" returns an array of significant matches with each element being a reference to [SR_protein, position,
motif, score]
See <http://rulai.cshl.edu/tools/ESE2/>
This the second implentation of Bio::SimpleAnalysisI which hopefully will make it easier to write wrappers on various services. This class
uses a web resource and therefore inherits from Bio::WebAgent.
SEE ALSO
Bio::SimpleAnalysisI, Bio::WebAgent
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHORS
Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
perl v5.14.2 2012-03-02 Bio::Tools::Analysis::DNA::ESEfinder(3pm)