Question: Generating Protein Consensus Sequence For Blast Input
2
gravatar for Ananth
9.0 years ago by
Ananth90
Ananth90 wrote:

I have a set of 3 protein sequences for which I need to find the "consensus sequence" which can be used as an input to blast against a local database.

how should I go about it?

blast • 5.3k views
ADD COMMENTlink written 9.0 years ago by Ananth90
1

Why not simply run 3 separate blast searches and compare & combine the results? There is no consensus AFAIK which can capture the whole complexity of the input set, so why bother?

ADD REPLYlink written 9.0 years ago by Darked894.2k

what did you find so far ?

ADD REPLYlink written 9.0 years ago by Pierre Lindenbaum122k

@Pierre: We are getting the expected results using EMBOSS programs :)

ADD REPLYlink written 9.0 years ago by Ananth90
6
gravatar for iw9oel_ad
9.0 years ago by
iw9oel_ad6.0k
iw9oel_ad6.0k wrote:

Are you sure that you wouldn't be better off making a profile of your sequences from a multiple alignment and using that to search your database, instead? E.g. using the EMBOSS program prophecy to create a profile from your multiply-aligned sequences and then using the EMBOSS program prophet to search your database.

ADD COMMENTlink modified 9.0 years ago • written 9.0 years ago by iw9oel_ad6.0k

Thanx for the suggestions ..

ADD REPLYlink written 9.0 years ago by Ananth90
4
gravatar for Simon Cockell
9.0 years ago by
Simon Cockell7.3k
Newcastle
Simon Cockell7.3k wrote:

If you have a multiple alignment of the sequences, you can load said alignment in JalView. JalView has a consensus line by default running along the bottom of alignment, you can right-click this and 'Copy consensus sequence'. Then you can paste the contents of your clipboard into a new text file - and you have your consensus sequence.

JalView Screenshot

It's a bit of a hack, and you're relying on JalView making a sensible consensus, but it will give you what you are after.

ADD COMMENTlink written 9.0 years ago by Simon Cockell7.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1575 users visited in the last hour