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Birong Hu

dblp:30/4474 · DBLP profile ↗
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1ranked-venue papers
0as first author
0since 2021 · last 2001
—ORCID · unresolved

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › multiple sequence alignment
alignment quality assessment		 0.012001
Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set · Bioinform. 2001
Bioinformatics and computational biology
multiple sequence alignment		 0.012001
Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set · Bioinform. 2001
Bioinformatics and computational biology
protein sequence analysis		 0.012001
Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set · Bioinform. 2001

Methods — techniques the papers use, named apart from their topics

hidden markov model · 0.0benchmark evaluation · 0.0
YearPublicationVenuePosition
2001 Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set
abstract
MOTIVATION: SAM-T99 is an iterative hidden Markov model-based method for finding proteins similar to a single target sequence and aligning them. One of its main uses is to produce multiple alignments of homologs of the target sequence. Previous tests of SAM-T99 and its predecessors have concentrated on the quality of the searches performed, not on the quality of the multiple alignment. In this paper we report on tests of multiple alignment quality, comparing SAM-T99 to the standard multiple aligner, CLUSTALW. RESULTS: The paper evaluates the multiple-alignment aspect of the SAM-T99 protocol, using the BAliBASE benchmark alignment database. On these benchmarks, SAM-T99 is comparable in accuracy with ClustalW. AVAILABILITY: The SAM-T99 protocol can be run on the web at http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-query.html and the alignment tune-up option described here can be run at http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-tuneup.html. The protocol is also part of the standard SAM suite of tools. http://www.cse.ucsc.edu/research/compbio/sam/
Kevin Karplus, Birong Hu
 Bioinform.2