Title |
Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST
|
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Published in |
BMC Biology, December 2006
|
DOI | 10.1186/1741-7007-4-41 |
Pubmed ID | |
Authors |
E Michael Gertz, Yi-Kuo Yu, Richa Agarwala, Alejandro A Schäffer, Stephen F Altschul |
Abstract |
TBLASTN is a mode of operation for BLAST that aligns protein sequences to a nucleotide database translated in all six frames. We present the first description of the modern implementation of TBLASTN, focusing on new techniques that were used to implement composition-based statistics for translated nucleotide searches. Composition-based statistics use the composition of the sequences being aligned to generate more accurate E-values, which allows for a more accurate distinction between true and false matches. Until recently, composition-based statistics were available only for protein-protein searches. They are now available as a command line option for recent versions of TBLASTN and as an option for TBLASTN on the NCBI BLAST web server. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United Kingdom | 1 | 33% |
United States | 1 | 33% |
Unknown | 1 | 33% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 2 | 67% |
Scientists | 1 | 33% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Canada | 2 | <1% |
Brazil | 2 | <1% |
United States | 2 | <1% |
Italy | 1 | <1% |
India | 1 | <1% |
Iceland | 1 | <1% |
Hungary | 1 | <1% |
Spain | 1 | <1% |
Belgium | 1 | <1% |
Other | 0 | 0% |
Unknown | 271 | 96% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 56 | 20% |
Researcher | 44 | 16% |
Student > Master | 38 | 13% |
Student > Bachelor | 38 | 13% |
Student > Doctoral Student | 14 | 5% |
Other | 29 | 10% |
Unknown | 64 | 23% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 85 | 30% |
Biochemistry, Genetics and Molecular Biology | 78 | 28% |
Computer Science | 8 | 3% |
Immunology and Microbiology | 6 | 2% |
Environmental Science | 6 | 2% |
Other | 21 | 7% |
Unknown | 79 | 28% |