BioPerl- blastcl3-parse the BLAST
Dear Seemann

I am new to Perl, and my background is Biology. I was wondering if you
could be of help with the follwoing problem.

1) I have downloaded NetBlast
2) I have Installed BioPerl
3) I have 36 fasta formate files (e.g. 1B94.fasta.txt, 1DNK.fasta.txt
and so on)
4) I want to write a Perl script that uses the blastcl3 program

ZBarjis@gmail.com Sat, 29 Nov 2008 19:25:06 UT

Suggestions of tools to study the 5'UTR region of genes
Hello,

I would like to analyze the 5' UTR region of several genes in order to
find interesting regulation sequences.
SInce it has been a while that I did not perform such a task, I would
like to know from people that I used to do it, what are the most
convenient software, webservers to use.

Fred Thu, 20 Nov 2008 07:24:08 UT

Exonerate and Genetic Code
Hello,

I used exonerate since 2 years (version 1.4), in particular the
prot2genome model, in order to define the locations of introns.

I test the new version (2.2) of exonerate.
The options --splice3 and --splice5 for change the splice score matrix
works perfectly.

But I have problem with the option --geneticcode !! When I used the

Natacha Tue, 18 Nov 2008 17:00:23 UT

SNP in NCBI & Ensemble
HI

I am searching snps of diffrent genes on both these site NCBI &
Ensemble.... I have a question which can be better explained through
example.... Like gene PTPN22 in human gave 344 SNPs in results and
ensemble gave 234 ? which one is more accurate?

And in NCBI I am also unable to find the location of SNP in genome

Iffy Mon, 17 Nov 2008 12:06:07 UT

Finding Gene DNA sequence
Hi

I have searched gene DNA sequence from NCBI and ENSEMBLE but I have
some quries either I got right sequence or not ..... Becoz in ensemble
their is diffrent sequence and in ncbi its diffrent .... In NCBI
entering the gene name I got two options for sequence that is FASTA
seq and GENEBANK sequence ....But those are also diffrent...How to

Iffy Wed, 12 Nov 2008 16:14:45 UT

Looking for a webservice that returns the nucleotide sequence of a human genome region
Dear all,

I am looking for a webservice that would return me the nucleotide
sequence of a given human genome region.
The ideal webservice would be that I just have to give the following
kind of parameters.
- The chromosome number (e.g. : 2)
- The nucleotide start position (e.g. : 128 000)
- The nucleotide end position (e.g. : 128 700)

Fred Wed, 12 Nov 2008 13:57:52 UT

protein sequence for all organism
Hello All,
I want to get the all the possible protein sequence for eukaryote.
I already downloaded nr from the NCBI ftp site, but i wish to have them
sorted by organism, one folder per species. Currently I am downloading data
from [link] . Does this
resource represent all the proteins sequences which are available in

Yvan Strahm Mon, 10 Nov 2008 13:18:51 UT

Bio C#
Dear fellow Bioinformaticians,

I have finally decided to release my version of Bio C#. It took me
more than three years to hone the design of the class library and an
unbearable amount of thought and headache. I even created Unit-tests
for the library which has a two-fold advantage. First the amount of

GoingSouth Thu, 06 Nov 2008 09:14:08 UT

How to find disease related SNPs?
Hello

I m working on disease named Alopecia areata and have 2 question:

1) I want to search SNPs for this disease. I have searched genes and
thier SNPs on NCBI but it gives all snps related to that gene.

2) In liturature search I have found some snp locations but how can i
locate that snp on gene?

Iffy Wed, 05 Nov 2008 08:12:40 UT

Hepatitis C Strains
Hi Guys,

Can somebody help with this one? I'm trying to create a classifier to
distinguish between various strains of Hep C and the medication that
can used to treat it. I've been told that there seems to be maybe
three or four (Asia, American, European & African).

I'm just not sure how to distinguish between the strains on NCIB or

Gavin Wed, 17 Sep 2008 07:59:03 UT

how to find phoshporylation sites
hello
can anybody tell me how to find phosphorylation sites in a protein

Amara Tue, 12 Aug 2008 03:45:46 UT

Understanding a database download
Hi Guys,

Pretty new to this as my next question will show. Is it possible to
achieve the following - I'm trying to download the dna sequence for
variations in mosquitos "Aedes aegypti" (or any variating species for
that matter) to my hard drive for analysis to try and identify the
variations between them for my final year project.

GavBio Wed, 13 Aug 2008 10:41:34 UT

finding interaction pathway of a gene
hello
can anybody tell me if there is any datbase or website from where i
can check interaction pathway of a gene

Amara Tue, 05 Aug 2008 04:47:34 UT

plot of basepairing probabilities
Hi,
I want to generate a RNAfold type dotplot of my base-match
probabilities for pair-wise alignment of RNAs. The probabilities could
be color coded or sizes of rectangles representing probabilities
should vary as in the case of RNAfold's dotplot.
Any ideas on how I could generate this using MATLAB, R or any other

tejajo Tue, 29 Jul 2008 08:22:42 UT

Connection to Database
Hi Guys,

Could somebody help with the following, is it possible to connect to a
database (FASTA etc.) from java code? and if so does anybody know how
its done.

Thanks for the help

Gavin

GavBio Mon, 28 Jul 2008 13:35:49 UT