Semi-automated update and cleanup of structural RNA alignment databases | Zendy

Jan Gorodkin | Zendy; Christian Zwieb | Zendy; Bjarne Knudsen | Zendy

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Semi-automated update and cleanup of structural RNA alignment databases

Author(s) -

Jan Gorodkin,

Christian Zwieb,

Bjarne Knudsen

Publication year - 2001

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/17.7.642

Subject(s) - database , computer science , genbank , consistency (knowledge bases) , rna , sequence database , sequence (biology) , data mining , artificial intelligence , biology , genetics , gene

We have developed a series of programs which assist in maintenance of structural RNA databases. A main program BLASTs the RNA database against GenBank and automatically extends and realigns the sequences to include the entire range of the RNA query sequences. After manual update of the database, other programs can examine base pair consistency and phylogenetic support. The output can be applied iteratively to refine the structural alignment of the RNA database. Using these tools, the number of potential misannotations per sequence was reduced from 20 to 3 in the Signal Recognition Particle RNA database.

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