Multiple Sequence Alignments.

Question

[chevivien]

Hallo. iam newbaby in Bioinformatics ..how do you know your multiple sequence alignment output is of good quality to be used for building HMM profiles.i have done BLAST searches using some gene family proteins and obtained around 450 sequences. then performed MSA using ClustalO ,but my output has alot of gaps..

Question ;how do i know if its of good quality to use for building hmm profiles?and if iam do use for building hmm profiles should i remove the gaps?

Answer 1

[Pappu]

Use gblocks to remove poorly aligned regions from the alignment: http://molevol.cmima.csic.es/castresana/Gblocks_server.html Why do you want to build HMM?

[chevivien]

thanks....i want to build hmm to be used for searching a sequence database to identify a particular gene family...

[Pappu]

The HMM you are looking for could already be in Pfam/SMART. It will be useful if the sequence similarity of the genes in the family is low. Otherwise blast will be good enough.