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Release 34.1 of ProDom, the Protein Domain database, was constructed by clustering homologous segments derived from 65,376 nonfragmentary sequences present in SWISS-PROT 34 as of May 21. Some 18,086 multiple alignments and consensus sequences for homologous domain families are provided. The enhanced Web user interface links to and from PROSITE and PDB. Domain families can be searched by keyword, and graphical representations of domain arrangements facilitate structural interpretation of large protein families.
All multiple alignments have been recalculated ab initio using the MultAlin program, and a new expertise procedure validates some domain boundaries. A sensitive homology search procedure scans all domain sequences in ProDom and retrieves matches with only one sequence for each domain family, thus drastically reducing output redundancy. The most significant matches are visualized graphically to assist with interpretation. For long queries, the former less-sensitive but faster search on consensus sequences is also provided. Users may choose between the classical NCBI BLAST 1.4.9 and the new WU-BLAST 2.0a13, which allows for gapped output (http://blast.wustl.edu). [Jerome Gouzy and Daniel Kahn (Centre National de la Recherche Scientifique-Institut National de la Recherche Agronomique |
| Author: Aaron Hall |
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Author Bio:
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| This article can be searched using: ProDom Release 34.1, Education & Learning, Pure Sciences, humanities social sciences |
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