hmmbuild function of HMMER
I am a computer engineering student. I am entitled for a project in HMMER on MIC Card. I wanted to know how is a profile made out of the .sto or .msf file using hmmbuild function in HMMER? I wanted to know the meaning of all the numbers calculated of matches, insertions and deletions and the way they are arranged at the output.
• 3,014 views
•
link
updated
by
Ram
•
written
by
medhi.banani •
•
written
by
medhi.banani •
1 answer
In a nutshell, hmmbuild builds a hidden markov model profile for a given set of aligned protein sequences.
To understand deeper, you might wanna dig through the web and read up on the following:
- Sequence homology
- Sequence alignment (with Multiple sequence alignment/analysis)
- Amino Acid substitution matrices
- Using HMMs to classify proteins
- The HMMER tutorial
These should help you get an idea of what HMMER is supposed to do and how it is supposed to achieve that. Feel free to ask more specific questions as you read up!
Log in to answer this question.
More posts like this
-
HMMER installed with conda: no tutorial folder
written by Wilber0x •
-
Problem in execution of the commands in HMMER
written by PriyaD •
-
Project for Master student
written by fabbrl •
-
Parse hmm(er) profiles in R
written by hivemind •
-
Determine characteristics(phenotype) from genomes
written by ahm3dhany •
-
Prototype Evaluation Survey of Inherited Disease Exploration System
written by lmanohara99 •
-
Don't get hits on HMMER
written by uguy •
-
Uses of HMMER in bioinformatics
written by medhi_banani •
-
Looking For An Rna Folding Algorithm In Java
written by nsrtsmhclk •
-
Investigating In A Gene/Protein ?
written by Giselle •
