HaMStR: Profile hidden markov model based search for orthologs in ESTs |
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Authors: | Ingo Ebersberger Sascha Strauss Arndt von Haeseler |
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Institution: | (1) Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, Vienna, Austria;(2) University of Vienna, Vienna, Austria;(3) Medical University of Vienna, Vienna, Austria;(4) University of Veterinary Medicine, Vienna, Austria |
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Abstract: | Background EST sequencing is a versatile approach for rapidly gathering protein coding sequences. They provide direct access to an organism's
gene repertoire bypassing the still error-prone procedure of gene prediction from genomic data. Therefore, ESTs are often
the only source for biological sequence data from taxa outside mainstream interest. The widespread use of ESTs in evolutionary
studies and particularly in molecular systematics studies is still hindered by the lack of efficient and reliable approaches
for automated ortholog predictions in ESTs. Existing methods either depend on a known species tree or cannot cope with redundancy
in EST data. |
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Keywords: | |
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