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In bioinformatics, BLAST (basic local alignment search tool) [3] is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences.
Distributed with the latest version of BLAST, this wrapper facilitates parallelization of the algorithm on modern hybrid architectures with many nodes and many cores within each node. [2] Protein: Burdyshaw CE, Sawyer S, Horton MD, Brook RG, Rekapalli B: 2017 CS-BLAST: Sequence-context specific BLAST, more sensitive than BLAST, FASTA, and SSEARCH.
BLAT can be used for alignments of two protein sequences. However, it is not the tool of choice for these types of alignments. BLASTP, the Standard Protein BLAST tool, is more efficient at protein-protein alignments; [1] Determination of the distribution of exonic and intronic regions of a gene; [9] [10]
The HH-suite comes with a number of pre-built profile HMMs that can be searched using HHblits and HHsearch, among them a clustered version of the UniProt database, of the Protein Data Bank of proteins with known structures, of Pfam protein family alignments, of SCOP structural protein domains, and many more.
BLAST is an algorithm used for calculating sequence similarity between biological sequences, such as nucleotide sequences of DNA and amino acid sequences of proteins. [7] BLAST is a powerful tool for finding sequences similar to the query sequence within the same organism or in different organisms.
A profile HMM modelling a multiple sequence alignment. HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. [2] Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments.
Computational analysis tools such as t-test, hierarchical clustering, self-organizing maps, regulatory network reconstruction, BLAST searches, pattern-motif discovery, protein structure prediction, structure-based protein annotation, etc.
Logo Expasy 2020. Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics.It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical ...