What is HMMER search?

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

What is a profile HMM used for?

A profile HMM is a variant of an HMM relating specifically to biological sequences. Profile HMMs turn a multiple sequence alignment into a position-specific scoring system, which can be used to align sequences and search databases for remotely homologous sequences.

What are the differences between HMMER and blast?

HMMER is mainly used for the finding the domain structure represented in the protein sequence. This can be useful over blast to find conserved remote homologs in your protein sequences. If your study has evolutionary significance, then you should go for HMMER over blast.

What is Kalign?

Kalign is an efficient multiple sequence alignment (MSA) program capable of aligning thousands of protein or nucleotide sequences. However, current alignment problems involving large numbers of sequences are exceeding Kalign’s original design specifications.

What is hmm file?

hmm” extension). It is an ASCII file containing a lot of header and descriptive records followed by large numerical matrix which holds probabilistic model of the motif. The file of this format is useful to search against sequnce databases to find out other proteins which share the same motif.

Why is multiple sequence alignment important?

Abstract. Multiple sequence alignment (MSA) has assumed a key role in comparative structure and function analysis of biological sequences. It often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families.

What is RPS BLAST?

RPS-BLAST is a variant of the PSI-BLAST program. Whereas PSI-BLAST first builds a PSSM that is used as a query for subsequent database searches, RPS-BLAST uses a protein sequence query to search a database of precalculated PSSMs in a single pass.

What is the difference between Phi-BLAST and Psi-BLAST?

PSI-BLAST considers position-specific information when searching for significant hits. PHI-BLAST uses a pattern, or profile, to seed an alignment, which is then extended by the normal BLASTP algorithm.

Why hidden Markov chain is applied?

A hidden Markov model (HMM) is a statistical model that can be used to describe the evolution of observable events that depend on internal factors, which are not directly observable.

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