SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
functional prediction SNP airtime Bioinformatics 1 10-24-2011 01:37 PM
plotSmear() function in edgeR Martin Umhang RNA Sequencing 1 01-25-2011 02:01 AM
Scripture score function wuj Bioinformatics 1 09-09-2010 06:21 AM
Function annotation Guedes General 0 06-18-2010 01:56 PM
function/abundance prediction from reads thedude Metagenomics 3 05-14-2009 10:23 PM

Reply
 
Thread Tools
Old 12-26-2011, 09:01 AM   #1
spark
Junior Member
 
Location: Dublin

Join Date: Mar 2009
Posts: 6
Default SNP function prediction in non-human species

Hello,

I'm trying predict SNP function for a few thousand non-synonymous coding sequence SNPs in cattle. I've looked through the documentation for SIFT and PolyPhen, but can't easily see if they can be configured to work with bovine genome data. Does anyone have any experience of using these or other tools for SNP function prediction in non-human species?

Thanks,

Stephen
spark is offline   Reply With Quote
Old 12-27-2011, 04:43 AM   #2
jeny
Member
 
Location: france

Join Date: Mar 2010
Posts: 16
Default

I am not sure if it could do what you want, but have you tried variant_effect_predistor of Ensembl http://www.ensembl.org/tools.html?
jeny is offline   Reply With Quote
Old 01-22-2012, 01:32 PM   #3
spark
Junior Member
 
Location: Dublin

Join Date: Mar 2009
Posts: 6
Default

Thanks for the suggestion. I've since used the Ensembl variant effect predictor, and it does something very similar to Annovar (which I've already used). The only difference is that the Ensembl program also outputs the amino acid residues for exonic SNPs.

What neither program does (and what I would like to do) is to use multiple sequence alignment data from many taxa to identify which SNPs affect highly conserved amino acid positions. Only tools like Sift and PolyPhen appear to do this, and I still haven't found a way to apply them to large batches of non-human data.

.

Last edited by spark; 01-22-2012 at 06:13 PM.
spark is offline   Reply With Quote
Old 03-20-2012, 06:48 AM   #4
clarissaboschi
Member
 
Location: US

Join Date: Apr 2010
Posts: 63
Default

Spark did you solve the problem?
I want to do the same, I installed the SIFT in Unix, but I did not find any information how should be the input file and command line. I know it is possible to perform with SIFT in Linux many sequences, but I don’t know how to do it.

I noticed that there are few databases when you install the SIFT for human, cattle, chicken, etc. So I think we need a list of all protein sequences with the substitutions, but I am not sure and I dont know what are the command lines...

Thanks
clarissaboschi is offline   Reply With Quote
Old 03-20-2012, 12:23 PM   #5
shoegame2001
Member
 
Location: California

Join Date: Dec 2010
Posts: 21
Default

Does anyone know if there is a SNP effect predictor for variants discovered in cDNA sequences for non-model organisms? I did a de novo transcriptome assembly and discovered variants in those data. No reference genome exists for my species. I can sort out synonymous vs. non-synonymous SNPs using BLAST to related species' proteins, but I was hoping for some more sophisticated prediction of the variant effect.

Given the discussion above, it sounds like it might not exist.
shoegame2001 is offline   Reply With Quote
Old 03-21-2012, 01:08 PM   #6
Dameon
Member
 
Location: St. Louis, MO - USA

Join Date: Dec 2011
Posts: 14
Default

Try using snpEff. If you have a reference_genome.fasta and either a .gff or .gtf file of the CDS regions, you can build your own custom database for SNP effect prediction. In the case of bovine, if the reference exists in Ensembl, the database can be easily downloaded in the latest version of snpEff.

http://snpeff.sourceforge.net/download.html
Dameon is offline   Reply With Quote
Old 03-21-2012, 09:15 PM   #7
shoegame2001
Member
 
Location: California

Join Date: Dec 2010
Posts: 21
Default

Okay, thanks. But no options if you don't have a reference genome?
shoegame2001 is offline   Reply With Quote
Old 01-22-2013, 01:45 AM   #8
Robby
Member
 
Location: Germany

Join Date: Mar 2011
Posts: 68
Default

Is there any tool, which predicts for each variant the probability, that this variant is damaging (like SIFT or PolyPhen for human). As far as I understand snpEff it just shows you the region of the variant and the effect like i.e. aminoacid-change, but not the damaging prediction score. I found also Mouse SNP Miner, but it seems, that this tools works just for known variants.
Robby is offline   Reply With Quote
Reply

Tags
cattle, function prediction, ngs, polyphen, sift

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:27 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO