Finding Similar Subsequences From Protein Sequences
Given a FASTA file of DNA-binding protein sequences only, I would like to find out if which motifs/subsequences are in a certain amount of sequences (at least 30% or more of them for example). These motifs do not need to be exact. Then after finding out these motifs, I would like to build a HMM model for these motifs.
I have already used HMMER + Pfam to find out domains of interest, but I suspect that some patterns may not be covered by Pfam. Is there any tool out there that can help me achieve this?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Getting A List Of Pfam Domains Involved in DNA-binding
written by jet •
-
Splitting a Protein Sequence in Domains
written by symela.lazaridi •
-
Use the Pfam database and a local database together to find protein domains
written by erick_rc93 •
-
Filtering HmmScan Domain Results
written by hewaholax •
-
Finding Proteins that have NO known Domains
written by ddofer •
-
Search/Align Homologs With The Same Architecture With Hmmer
written by User 9501 •
-
Identifying Multiple Domains Using Hmmer 3.0
written by Hari •
-
Mapping Protein Domains To Exons
written by Anupam Sinha •
-
Domain Search Using Hmmer
written by Hari •
-
Method For Randomly Selecting Subsequences In An Alignment ?
written by Spyros •
