Table of Contents
What is a profile HMM?
Profile HMMs. 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 HMMs and how do they work?
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.
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Can profile HMM acceleration heuristics be more sensitive than blast?
The challenge is that to preserve the significant yet narrow gain in sensitivity that profile HMM methods show over BLAST [28] – [30], any useful profile HMM acceleration heuristic must be more sensitive than BLAST’s already excellent heuristics.
Can a profile hidden Markov model (HMM) be used for pairwise alignment?
Results: We have generalized the alignment of protein sequences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile HMMs. We present a method for detecting distant homologous relationships between proteins based on this approach.
What are the different types of HMM search?
The four search types phmmer, hmmsearch, hmmscan and jackhmmer are supported (see Programs ). The search function accepts single sequences as well as sequence alignments or profile HMMs. The search results are accompanied by a report on the taxonomic breakdown, and the domain organisation of the hits.
Profile HMMs are probabilistic models that encapsulate the evolutionary changes that have occurred in a set of related sequences (i.e. a multiple sequence alignment). To do so, they capture position-specific information about how conserved each amino acid is in each column of the alignment, see Figure 2.
What is an 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.
What is hmm scan?
HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments. It detects homology by comparing a profile-HMM to either a single sequence or a database of sequences.
What is hmm length?
The length of the HMM should be the average of the length of the sequences. The above sequences are of lengths 3, 2, 3 and 5, respectively, yielding an average of 3.25.
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 are the different Hidden Markov Models?
After reviewing the basic concept of HMMs, we introduce three types of HMM variants, namely, profile-HMMs, pair-HMMs, and context-sensitive HMMs, that have been useful in various sequence analysis problems. Section 3 provides an overview of profile hidden Markov models and their applications.
How do I open an HMM file?
The Four Best Ways to Open HMM Files
- Pick the Right Program. Start by choosing the right program to open your HMM file.
- Note the File Type. Other programs may be able to open your HMM file, depending on the type of file it is.
- Ask the Developer.
- Use a Universal File Viewer.
- Recommended Download.
What is Kalign?
Kalign is an efficient multiple sequence alignment (MSA) program capable of aligning thousands of protein or nucleotide sequences. The new version maintains high alignment accuracy on both protein and nucleotide alignments and scales better than other MSA tools.