Sensitivity and selectivity in protein similarity searches: a comparison of Smith-Waterman in hardware to BLAST and FASTA.
- Computer ScienceGenomics
It is demonstrated here that the Smith-Waterman (S-W) dynamic programming method and the optimized version of FASTA are significantly better able to distinguish true similarities from statistical noise than is the popular database search tool BLAST.
The Fasta and Blast programs
- Computer Science
The programs from the Blast and Fasta families are heuristics that reduce computation time by sacri cing some sensitivity: they reduce the size of the problem by selecting the sequences of the database that are thought to share signi cant similarity with the query sequence, and by locating the similarity regions inside the sequences.
Fast and sensitive protein sequence homology searches using hierarchical cluster BLAST
- Computer Science, BiologybioRxiv
This work presents a pipeline that improves the speed of amino acid sequence homology searches with a minimal decrease in sensitivity and specificity by searching against hierarchical clusters.
Kalign – an accurate and fast multiple sequence alignment algorithm
- BiologyBMC Bioinformatics
Kalign, a method employing the Wu-Manber string-matching algorithm, is developed to improve both the accuracy and speed of multiple sequence alignment and is especially well suited for the increasingly important task of aligning large numbers of sequences.
Bioinformatics with basic local alignment search tool (BLAST) and fast alignment (FASTA)
This paper provides an analysis of BLAST and FASTA in sequence analysis and suggests that BLAST appears to be faster and also more accurate than FasTA.
Comparison of DNA sequences with protein sequences.
FASTX and FASTY are used to scan the Mycoplasma genitalium, Haemophilus influenzae, and Methanococcus jannaschii genomes for unidentified or misidentified protein-coding genes and are found to be quite accurate, except when an out-of-frame translation produces a low-complexity protein sequence.
Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.
SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments
- Computer ScienceBioinform.
A new algorithm has been devised for the computation of a gapped alignment of two sequences using dynamic programming to build an accurate alignment based on the fragments initially identified.
PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology
- Computer ScienceNucleic Acids Res.
PARALIGN is a rapid and sensitive similarity search tool for the identification of distantly related sequences in both nucleotide and amino acid sequence databases. Two algorithms are implemented,…
Biological Evaluation of d2, an Algorithm for High-Performance Sequence Comparison
- Computer ScienceJ. Comput. Biol.
This work demonstrates that d2 is a unique, sensitive, and selective method of rapid sequence comparison that can detect novel sequence relationships which remain undetected by alternate methodologies.
SHOWING 1-10 OF 10 REFERENCES
Rapid and sensitive protein similarity searches.
An algorithm was developed which facilitates the search for similarities between newly determined amino acid sequences and sequences already available in databases and increases sensitivity by giving high scores to those amino acid replacements which occur frequently in evolution.
A general method applicable to the search for similarities in the amino acid sequence of two proteins.
- BiologyJournal of molecular biology
Efficient algorithms for folding and comparing nucleic acid sequences
- BiologyNucleic Acids Res.
The homology and secondary structure programs are respectively illustrated with a comparison of two phage genomes, and a discussion of Drosophila melanogaster 55 RNA folding.
The LDL receptor gene: a mosaic of exons shared with different proteins.
The LDL receptor appears to be a mosaic protein built up of exons shared with different proteins, and it therefore belongs to several supergene families.
Glutathione transferases--structure and catalytic activity.
- Biology, ChemistryCRC critical reviews in biochemistry
The glutathione transferases are recognized as important catalysts in the biotransformation of xenobiotics, including drugs as well as environmental pollutants. Multiple forms exist, and numerous…
Cloning of the gene and cDNA for mammalian β-adrenergic receptor and homology with rhodopsin
Cloning of the gene and cDNA for the mammalian β2AR indicates significant amino-acid homology with bovine rhodopin and suggests that, like rhodopsin7, βAR possesses multiple membrane-spanning regions.
On the Theory and Computation of Evolutionary Distances
- Computer Science
The algorithm, introduced here, lends itself to computer programming and provides a method to compute evolutionary distance which is shorter than the other methods currently in use.
Structure and function of voltage-sensitive ion channels.
Experimental results have begun to define a functional map of voltage-sensitive Na+ and Ca2+ channels, and coordinated application of biochemical, biophysical, and molecular genetic methods should lead to a clear understanding of the molecular basis of electrical excitability.
Adrenergic receptors. Models for the study of receptors coupled to guanine nucleotide regulatory proteins.
- BiologyThe Journal of biological chemistry