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Basic Linear Algebra Subprograms (BLAS) is a specification that prescribes a set of low-level routines for performing common linear algebra operations such as vector addition, scalar multiplication, dot products, linear combinations, and matrix multiplication.
The task addressed by BLAST is the need to check whether software satisfies the behavioral requirements of its associated interfaces. BLAST employs counterexample -driven automatic abstraction refinement to construct an abstract model that is then model-checked for safety properties.
To help users interpreting BLAST results, different software is available. According to installation and use, analysis features and technology, here are some available tools: [30] NCBI BLAST service; general BLAST output interpreters, GUI-based: JAMBLAST, Blast Viewer, BLASTGrabber; integrated BLAST environments: PLAN, BlastStation-Free ...
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.
formatdb must be used in order to format protein or nucleotide source databases before these databases can be searched by BLAST. [2] The source database may be in either FASTA or ASN.1 format. Although the FASTA format is most often used as input to formatdb, the use of ASN.1 is advantageous for those who are using ASN.1 as the common source ...
The user provides a proteome in fasta format, and the system employs Psi-blast, Psipred and Modeller to predict protein function and subcellular localization. Proteome Analyst uses machine-learned classifiers to predict things such as GO molecular function. User-supplied training data can also be used to create custom classifiers. (bio.tools entry)
The web-based application of BLAT can be accessed from the UCSC Genome Bioinformatics Site. [8] Building the index is a relatively slow procedure. Therefore, each genome assembly used by the web-based BLAT is associated with a BLAT server, in order to have a pre-computed index available for alignments.
The project mode is used in more difficult cases, when manual corrections of target-template alignments are needed to improve the quality of the resulting model. In this mode the input is a project file that can be generated by the DeepView (Swiss Pdb Viewer) visualization and structural analysis tool, [ 4 ] to allow the user to examine and ...