What is HHpred used for?
HHpred is a fast server for remote protein homology detection and structure prediction and is the first to implement pairwise comparison of profile hidden Markov models (HMMs). It allows to search a wide choice of databases, such as the PDB, SCOP, Pfam, SMART, COGs and CDD.
Table of Contents
What is a bioinformatics toolkit?
The MPI Bioinformatics Toolkit is an interactive web service which offers access to a great variety of public and in-house bioinformatics tools. They are grouped into different sections that support sequence searches, multiple alignment, secondary and tertiary structure prediction and classification.
What is PSI-BLAST good for?
This PSSM is used to further search the database for new matches, and is updated for subsequent iterations with these newly detected sequences. Thus, PSI-BLAST provides a means of detecting distant relationships between proteins.
What is BLAST program?
Introduction. BLAST is an acronym for Basic Local Alignment Search Tool and refers to a suite of programs used to generate alignments between a nucleotide or protein sequence, referred to as a “query” and nucleotide or protein sequences within a database, referred to as “subject” sequences.
Which software is used in bioinformatics?
List of open-source bioinformatics software
| Software | Description | License |
|---|---|---|
| .NET Bio | Language-neutral toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists | Apache |
| AMPHORA | Metagenomics analysis software | GPL |
| Anduril | Component-based workflow framework for data analysis | GPL |
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.
How do BLAST work?
How does BLAST work? BLAST identifies homologous sequences using a heuristic method which initially finds short matches between two sequences; thus, the method does not take the entire sequence space into account. After initial match, BLAST attempts to start local alignments from these initial matches.
What is HHpred?
HHpred is a fast server for remote protein homology detection and structure prediction and is the first to implement pairwise comparison of profile hidden Markov models (HMMs).
What types of databases does HHpred offer?
The HHpred server and the HH-suite software package offer many popular, regularly updated databases, such as the Protein Data Bank, as well as the InterPro, Pfam, Clusters of Orthologous Groups (COG), and SCOP databases.
What can HHpred do for You?
HHpred can produce pairwise query-template alignments, multiple alignments of the query with a set of templates selected from the search results, as well as 3D structural models that are calculated by the MODELLER software from these alignments. Report a missing or misdirected URL.
What are the different alignment options in HHpred?
Search options include local or global alignment and scoring secondary structure similarity. HHpred can produce pairwise query-template alignments, multiple alignments of the query with a set of templates selected from the search results, as well as 3D structural models that are calculated by the MODELLER software from these alignments.
