BLAST

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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&nbsp;<ref name="BLAST webpage">http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>.&nbsp;&nbsp;  
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BLAST is a [[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&nbsp;<ref name="BLAST webpage">http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>.&nbsp;&nbsp;  
  
 
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|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 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|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.  
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&nbsp; <ref>Information for the table taken from http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>  
 
&nbsp; <ref>Information for the table taken from 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|protein sequence]]&nbsp;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&nbsp;<ref name="BLAST webpage">http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>.&nbsp; Links to these programs can be found in the table above.  
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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|protein sequence]]&nbsp;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&nbsp;<ref name="BLAST webpage">http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>.&nbsp; Links to these programs can be found in the table above.  
  
 
== Specialised Blast Programs  ==
 
== Specialised Blast Programs  ==

Revision as of 20:12, 14 October 2013

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:  


A Table Showing a Brief Description of the Five Basic Blast Programmes
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

  [2]

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.

References

  1. 1.0 1.1 http://blast.ncbi.nlm.nih.gov/Blast.cgi
  2. Information for the table taken from http://blast.ncbi.nlm.nih.gov/Blast.cgi
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