Identification and Application of Biological Repetitive Sequences
Repetitive sequences are abundant in both genomes and proteins. Identification and application of such biological repetitive sequences are important in Biology for at least two reasons. First, repetitive sequences play important roles in evolution. Second, they present difficulties to genome/protein analyses such as genome assembly and sequence alignment. The exciting related research projects that we have done or have been working on include
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identifying low-complexity regions in protein sequences;
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application of low-complexity regions to sequence similarity search in large biological databases;
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identifying repetitive sequences in sequenced genomes;
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identifying repetitive sequences in genomic fragments.
Software
TBA
People
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Xuehui Li
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Tamer Kahveci
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A. Mark Settles
Publications
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Xuehui Li, Tamer Kahveci and Mark Settles,
A Novel
Genome-Scale Repeat Finder Geared towards Transposons,
accepted to Bioinformatics, 2007.
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Xuehui Li, Tamer Kahveci,
Quality-based similarity search
for biological sequence databases,
BIOCOMP, 2007
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Xuehui Li, Tamer Kahveci
A Novel Algorithm for
Identifying Low-complexity Regions in a Protein Sequence
Bioinformatics 22:24 (2006), 2980-2987 (PubMed)
(Bioinformatics)
Funding
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UF Research Initiatives (Project #: 00072365)
Identification of Repeats in Genomes In the Prescence of
transposons.(05/01/2008-04/30/2010)
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UFGI
seed grant (Project #: 00060495),
Sequence indexed
maize transposon insertion sites for cereal functional
genomics. (01/23/2006 - 6/30/2008)
Tamer Kahveci
Last modified: Fri Aug 15 16:02:58 EDT 2008