SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Multiple alignment why and what for (Bowtie -k options) pmcqt Bioinformatics 0 11-29-2011 06:48 AM
Align multiple sequences in tabular or fasta format pchiang Bioinformatics 7 07-01-2011 11:18 PM
GALAXY: Huge amount of data? sklages Bioinformatics 1 04-12-2011 06:03 AM
Mapping against multiple sequences michaelDP Metagenomics 2 10-15-2010 10:22 AM
Reducing amount of sequences graham90978 Illumina/Solexa 0 10-09-2010 05:23 PM

Reply
 
Thread Tools
Old 05-03-2011, 09:04 PM   #1
LucasVS
Junior Member
 
Location: Australia

Join Date: May 2011
Posts: 1
Default Multiple Alignment software for huge amount of peptide sequences/cysteine framework

***edit***

Last edited by LucasVS; 04-15-2012 at 11:25 PM.
LucasVS is offline   Reply With Quote
Old 05-06-2011, 07:20 AM   #2
colindaven
Senior Member
 
Location: Germany

Join Date: Oct 2008
Posts: 415
Default

I wouldn't align with Excel .... scripts are very slow in it, and I doubt you'll find a bioinformatician willing to touch it!

Why not try muscle, thats a nice quick bit of software. Perhaps muscle can also align cysteines only, with the gap characters (-) you put in. Otherwise maybe subsitute all other amino acids with a fairly neutral amino acid (perhaps Alanine). You can then see if the alignment is mainly determined by the cysteines.
colindaven is offline   Reply With Quote
Old 05-09-2011, 01:40 AM   #3
me_myself_andI
Member
 
Location: Singapore

Join Date: Nov 2010
Posts: 30
Default

Hello,

Excel for storing sequence data and/or VBA for scripting is a very bad idea in this context.

Try the following:
Convert your sequences to Fasta format (plain text) and use either Muscle (muscle -maxiters 1 -in your-fasta-file) or Mafft (mafft -auto your-fasta-file)

Andreas
me_myself_andI is offline   Reply With Quote
Old 03-28-2012, 08:15 PM   #4
*#1*
Junior Member
 
Location: East coast

Join Date: Jul 2010
Posts: 8
Default

I also suggest Muscle http://www.drive5.com/muscle/
*#1* is offline   Reply With Quote
Reply

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 02:41 AM.


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