Question: Searching Homology (Blast)
gravatar for onpelikan
6.9 years ago by
onpelikan0 wrote:

Hi, I need to analyze protein mutations via MAPP tool. For this tool I need have multiple alignemnt file and phylogenetic tree file. So I need to obtain homology sequences, but not so closely related ones, because closely related sequences are not significat for MAPP. How to use BLAST to find not so close related homolgies. I tried use PSI-BLAST but:

  1. How many iteration is needed?
  2. Is inclusion_ethresh param significant?
ADD COMMENTlink modified 6.4 years ago by Biostar ♦♦ 20 • written 6.9 years ago by onpelikan0

There are many ways to measure protein mutations, so I'm unclear why you need to use MAPP. Of course you'll need to have a curated alignment to assume homology, but are you asking how to get a phylogenetically diverse array of sequences in a given lineage?

ADD REPLYlink written 6.9 years ago by Josh Herr5.7k
gravatar for Nari
6.9 years ago by
United States
Nari880 wrote:

Blast will not give you alignment file and tree file as output.
Clustalw2 executable file can help you.
Options are available for different outputs of alignment and tree files.

MAPP requires
1.fasta alignment file which matches with alignment.fas obtained from clustalw2
2.tree file which matches with tree.dnd obtained from clustalw2

Use these files for running MAPP:
Here is your code. for windows cmd:

java -jar MAPP.jar -f alignment.fas -t tree.dnd -o out.txt


ADD COMMENTlink modified 6.9 years ago • written 6.9 years ago by Nari880

Thank you for your answer but my question is about psi-blast. How to obtain not so closely related sequences? For multiple sequence alignment I'm using Clustal Omega and for tree I'm using SEMPHY (it is not very well. Probably MEGA or PhyML would be better for tree reconstruction).

ADD REPLYlink written 6.9 years ago by onpelikan0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1150 users visited in the last hour