Improved tools for biological sequence comparison.
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TLDR
Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.Abstract:
We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a "graphic matrix" plot or as individual alignments. In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternative scoring matrices.read more
Citations
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BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results.
TL;DR: This work has created new data bases of conserved regions and functional domains for protein sequences in NCBI's Entrez data base, and BEAUTY allows this information to be incorporated directly into BLAST search results.
Journal ArticleDOI
Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments
Hongyi Zhou,Yaoqi Zhou +1 more
TL;DR: The resulting method, called SP3, is found to be the most sensitive and accurate single‐method server in all benchmarks tested where other methods are available for comparison and its accuracy rivals some of the consensus methods such as ShotGun‐INBGU, Pmodeller3, Pcons4, and ROBETTA.
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Regulation of the Bacillus subtilis alsS, alsD, and alsR genes involved in post-exponential-phase production of acetoin.
TL;DR: Transcriptional fusions to alsS and alsR revealed that AlsR is required for the transcription of the alsSD operon, which increases during stationary phase, and two mutations that cause increased expression of theAls SD operon have been isolated, cloned, and sequenced.
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Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World
Hideki Hirakawa,Kenta Shirasawa,Koji Miyatake,Tsukasa Nunome,Satomi Negoro,Akio Ohyama,Hirotaka Yamaguchi,Shusei Sato,Sachiko Isobe,Satoshi Tabata,Hiroyuki Fukuoka +10 more
TL;DR: The detailed comparative analysis of the eggplant and tomato genomes will facilitate the understanding of the genomic architecture of solanaceous plants, which will contribute to cultivation and further utilization of these crops.
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Cloning and characterization of ECE1, a gene expressed in association with cell elongation of the dimorphic pathogen Candida albicans
TL;DR: The gene ECE1 (extent of cell elongation 1) was isolated by differential hybridization screening of a Candida albicans cDNA library by using probes derived from populations of yeast cells or hyphae and showed no discernible homology with other known sequences.
References
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A general method applicable to the search for similarities in the amino acid sequence of two proteins
TL;DR: A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed and it is possible to determine whether significant homology exists between the proteins to trace their possible evolutionary development.
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TL;DR: This letter extends the heuristic homology algorithm of Needleman & Wunsch (1970) to find a pair of segments, one from each of two long sequences, such that there is no other Pair of segments with greater similarity (homology).
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Rapid and sensitive protein similarity searches
TL;DR: 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.
Journal ArticleDOI
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W. J. Wilbur,David J. Lipman +1 more
TL;DR: An algorithm for the global comparison of sequences based on matching k-tuples of sequence elements for a fixed k results in substantial reduction in the time required to search a data bank when compared with prior techniques of similarity analysis, with minimal loss in sensitivity.