Increased coverage obtained by combination of methods for protein sequence database searching
نویسندگان
چکیده
منابع مشابه
Increased Coverage Obtained by Combination of Methods for Protein Sequence Database Searching
MOTIVATION Sequence alignment methods that compare two sequences (pairwise methods) are important tools for the detection of biological sequence relationships. In genome annotation, multiple methods are often run and agreement between methods taken as confirmation. In this paper, we assess the advantages of combining search methods by comparing seven pairwise alignment methods, including three ...
متن کاملComparison of methods for searching protein sequence databases.
We have compared commonly used sequence comparison algorithms, scoring matrices, and gap penalties using a method that identifies statistically significant differences in performance. Search sensitivity with either the Smith-Waterman algorithm or FASTA is significantly improved by using modern scoring matrices, such as BLOSUM45-55, and optimized gap penalties instead of the conventional PAM250 ...
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The Blocks Database WWW (http://blocks.fhcrc.org ) and Email ([email protected] ) servers provide tools to search DNA and protein queries against the Blocks+ Database of multiple alignments, which represent conserved protein regions. Blocks+ nearly doubles the number of protein families included in the database by adding families from the Pfam-A, ProDom and Domo databases to those from PR...
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We have recently developed a flexible protein structure alignment program (FATCAT) that identifies structural similarity, at the same time accounting for flexibility of protein structures. One of the most important applications of a structure alignment method is to aid in functional annotations by identifying similar structures in large structural databases. However, none of the flexible struct...
متن کاملSIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage
The Similarity Matrix of Proteins (SIMAP, http://mips.gsf.de/simap/) database has been designed to massively accelerate computationally expensive protein sequence analysis tasks in bioinformatics. It provides pre-calculated sequence similarities interconnecting the entire known protein sequence universe, complemented by pre-calculated protein features and domains, similarity clusters and functi...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2003
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btg156