RSEARCH: Finding homologs of single structured RNA sequences View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2003-12

AUTHORS

Robert J Klein, Sean R Eddy

ABSTRACT

BACKGROUND: For many RNA molecules, secondary structure rather than primary sequence is the evolutionarily conserved feature. No programs have yet been published that allow searching a sequence database for homologs of a single RNA molecule on the basis of secondary structure. RESULTS: We have developed a program, RSEARCH, that takes a single RNA sequence with its secondary structure and utilizes a local alignment algorithm to search a database for homologous RNAs. For this purpose, we have developed a series of base pair and single nucleotide substitution matrices for RNA sequences called RIBOSUM matrices. RSEARCH reports the statistical confidence for each hit as well as the structural alignment of the hit. We show several examples in which RSEARCH outperforms the primary sequence search programs BLAST and SSEARCH. The primary drawback of the program is that it is slow. The C code for RSEARCH is freely available from our lab's website. CONCLUSION: RSEARCH outperforms primary sequence programs in finding homologs of structured RNA sequences. More... »

PAGES

44

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-4-44

DOI

http://dx.doi.org/10.1186/1471-2105-4-44

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1048914023

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/14499004


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