SciCombinator

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Concept: Smith–Waterman algorithm

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We propose SW#, a new CUDA GPU enabled and memory efficient implementation of dynamic programming algorithms for local alignment. It can be use as either a standalone application or a library. Although there are other GPU implementations of the Smith-Waterman algorithm, SW# is the only one publicly available that can produce sequence alignments on genome-wide scale. For long sequences, it is at least a few hundred times faster than a CPU version of the same algorithm.

Concepts: Algorithm, Computer, Computer program, Computer programming, Dynamic programming, BLAST, Smith–Waterman algorithm, Levenshtein distance

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The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology (NCBI) is an important resource for searching and aligning sequences. A new BLAST report allows faster loading of alignments, adds navigation aids, allows easy downloading of subject sequences and reports and has improved usability. Here, we describe these improvements to the BLAST report, discuss design decisions, describe other improvements to the search page and database documentation and outline plans for future development. The NCBI BLAST URL is http://blast.ncbi.nlm.nih.gov.

Concepts: Bioinformatics, Computational phylogenetics, Searching, Sequence alignment, Dynamic programming, BLAST, FASTA, Smith–Waterman algorithm

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Short half-life is one of the key challenges in the field of therapeutic peptides. Various studies have reported enhancement in the stability of peptides using methods like chemical modifications, D-amino acid substitution, cyclization, replacement of labile aminos acids, etc. In order to study this scattered data, there is a pressing need for a repository dedicated to the half-life of peptides. To fill this lacuna, we have developed PEPlife (http://crdd.osdd.net/raghava/peplife), a manually curated resource of experimentally determined half-life of peptides. PEPlife contains 2229 entries covering 1193 unique peptides. Each entry provides detailed information of the peptide, like its name, sequence, half-life, modifications, the experimental assay for determining half-life, biological nature and activity of the peptide. We also maintain SMILES and structures of peptides. We have incorporated web-based modules to offer user-friendly data searching and browsing in the database. PEPlife integrates numerous tools to perform various types of analysis such as BLAST, Smith-Waterman algorithm, GGSEARCH, Jalview and MUSTANG. PEPlife would augment the understanding of different factors that affect the half-life of peptides like modifications, sequence, length, route of delivery of the peptide, etc. We anticipate that PEPlife will be useful for the researchers working in the area of peptide-based therapeutics.

Concepts: Protein, Amino acid, Peptide, Experiment, Determinacy, BLAST, Smith–Waterman algorithm

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The Basic Local Alignment Search Tool (BLAST) algorithm remains one of the most widely used bioinformatic programs. For many projects, new sequencing technologies and increased database sizes will increase the BLAST output significantly. Frequently, this output is so large that it is no longer able to be processed manually. As BLAST users are increasingly recruited from mainstream biology without any bioinformatic background, user-friendly programs capable of BLAST output visualization, analysis and post-processing are in demand. In this review, freely available BLAST output processing programs are categorized as BLAST output interpreters, BLAST environments, BLAST output parsers or specialized tools. They are evaluated according to their user-friendliness, analysis features and high-throughput data processing capabilities.

Concepts: Bioinformatics, Molecular biology, Data, Computer program, Sequence alignment, Usability, BLAST, Smith–Waterman algorithm