BLAST: Difference between revisions
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BLAST is a [[Primary sequence database|primary sequence database]] that enables you to compare a [[DNA|DNA]] or [[Protein|protein]] sequence of interest to other known sequences, allowing you to find regions of similarity between them <ref name="BLAST webpage">http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>. | BLAST is a [[Primary sequence database|primary sequence database]] that enables you to compare a [[DNA|DNA]] or [[Protein|protein]] sequence of interest to other known sequences, allowing you to find regions of similarity between them <ref name="BLAST webpage">http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>. | ||
The results of a BLAST search give a graphic summary of the amount of alignment between the query sequence and the sequence hits from the database. The database sequences which produce significant allignments are shown in a table, which tells you the protein that the sequence codes for. Each has an accession number; clicking on this accession number allows you to see the souce organism of the protien, as well as giving links to papers on the protein. The E value (Expect value) is the staistical significance threshold; it gives the number of hits that are likely to be found by chance, therefore a lower E value will result in better matches as the probability of a chance result is less. | |||
The Blast web page can be found at: http://blast.ncbi.nlm.nih.gov/Blast.cgi | |||
== Basic Blast Programs == | == Basic Blast Programs == | ||
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| Search protein database using a protein query | | Search protein database using a protein query | ||
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| blastx | | [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&BLAST_PROGRAMS=blastx&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome blastx] | ||
| Search protein database using a translated nucleotide query | | Search protein database using a translated nucleotide query | ||
|- | |- | ||
| tblastn | | [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&BLAST_PROGRAMS=tblastn&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome tblastn] | ||
| Search translated nucleotide database using a protein query | | Search translated nucleotide database using a protein query | ||
|- | |- | ||
| tblastx | | [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&BLAST_PROGRAMS=tblastx&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome tblastx] | ||
| Search translated nucleotide database using a translated nucleotide query | | Search translated nucleotide database using a translated nucleotide query | ||
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BlastP, allows you to compare an [[Amino acid|amino acid]] query sequence against a protein database. BlastN enables you to look at a [[Nucleotide|nucleotide]] query sequence against a nucleotide sequence database. Using BlastX you can compare a nucleotide query sequence translated in all [[Reading frame|reading frames]] against a protein sequence database. With tBlastN you can see the similarites between a [[Protein|protein]] query sequence and nucleotide sequences from the database, dynamically translated in all reading frames, and finally, tBlastX allows you to compare the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database <ref name="BLAST webpage">http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>. | BlastP, allows you to compare an [[Amino acid|amino acid]] query sequence against a protein database. BlastN enables you to look at a [[Nucleotide|nucleotide]] query sequence against a nucleotide sequence database. Using BlastX you can compare a nucleotide query sequence translated in all [[Reading frame|reading frames]] against a protein sequence database. With tBlastN you can see the similarites between a [[Protein|protein]] query sequence and nucleotide sequences from the database, dynamically translated in all reading frames, and finally, tBlastX allows you to compare the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database <ref name="BLAST webpage">http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>. Links to these programs can be found in the table above. | ||
== Specialised Blast Programs == | |||
There is also the option to perform more specialized BLAST searches such as a primer BLAST search. Links for these searches can be found below to main BLAST search links. | |||
=== References === | === References === | ||
<references /> | <references /> | ||
Revision as of 10:47, 16 November 2011
BLAST is a primary sequence database that enables you to compare a DNA or protein sequence of interest to other known sequences, allowing you to find regions of similarity between them [1].
The results of a BLAST search give a graphic summary of the amount of alignment between the query sequence and the sequence hits from the database. The database sequences which produce significant allignments are shown in a table, which tells you the protein that the sequence codes for. Each has an accession number; clicking on this accession number allows you to see the souce organism of the protien, as well as giving links to papers on the protein. The E value (Expect value) is the staistical significance threshold; it gives the number of hits that are likely to be found by chance, therefore a lower E value will result in better matches as the probability of a chance result is less.
The Blast web page can be found at: http://blast.ncbi.nlm.nih.gov/Blast.cgi
Basic Blast Programs
There are 5 different BLAST programmes depending on the type of sequence you are studying.
| Nucleotide blast (blastn) | Search a nucleotide database using a nucleotide query |
| Protein blast (blastp) | Search protein database using a protein query |
| blastx | Search protein database using a translated nucleotide query |
| tblastn | Search translated nucleotide database using a protein query |
| tblastx | Search translated nucleotide database using a translated nucleotide query |
BlastP, allows you to compare an amino acid query sequence against a protein database. BlastN enables you to look at a nucleotide query sequence against a nucleotide sequence database. Using BlastX you can compare a nucleotide query sequence translated in all reading frames against a protein sequence database. With tBlastN you can see the similarites between a protein query sequence and nucleotide sequences from the database, dynamically translated in all reading frames, and finally, tBlastX allows you to compare the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database [1]. Links to these programs can be found in the table above.
Specialised Blast Programs
There is also the option to perform more specialized BLAST searches such as a primer BLAST search. Links for these searches can be found below to main BLAST search links.