Blast Help : GeneDB

T. brucei Blast Help

Saturday July 26th 2008
Due to essential systems work, GeneDB will be unavailable on this day from around 9:30am BST to early afternoon

July 23rd 2008
Please note: We are experiencing problems with downloading Boolean search results. Additonally, the number of annotations reported to GO terms displayed on the gene page and as returned by Boolean searches is incorrect. We are working to fix these problems.


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This section is designed to

aid users in the applications of BLAST/omniBLAST
inform users about the databases available for similarity searching
direct users to alternative BLAST servers

Information on BLAST/omniBLAST:

BLAST

BLAST (Basic Local Alignment Search Tool) is an algorithm used by a family of 5 programs (blastp, blastn, blastx, tblastn, tblastx) that will locally align your query sequence against sequences in a molecular database. The BLAST output reports alignments (i.e. sequences in the database that are identical/similar to your query sequence).

blastp
compares an amino acid query sequence against a protein sequence database
blastn
compares a nucleotide query sequence against a nucleotide sequence database
blastx
compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database
tblastn
compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands)
tblastx
compares the six-frame translations of a nucleo- tide query sequence against the six-frame transla- tions of a nucleotide sequence database.

During similarity searching, BLAST programs first look for similar segments (high-scoring segment pairs or HSPs) between the query sequence and a database sequence and then evaluate the statistical significance of any matches that were found, finally reporting only those matches that satisfy a user-selectable threshold of significance (see the BLAST help manual for more explanation). The sensitivity and speed of the programs can be adjusted via the standard BLAST algorithm parameters, selectivity of the programs can be adjusted via the cutoff score. The alignments are reported in order of significance as judged by the statistical method applied.
There are two versions of BLAST, BLAST [1] and BLAST 2.0 [2] (which amongst other modifications supports gapped alignments), neither of these is however suitable for searching with very short fragments (for example as carried out in motif searching). For this purpose, a separate protein motif search facility has also been integrated into GeneDB. The BLAST searches available through GeneDB and the Sanger Project pages use BLAST 2.0.

If you would like to find out more about BLAST and the mathematical models used to compute the alignments and scores, here are some useful tutorials/websites:
1. http://www.sanger.ac.uk/HGP/help/blast.shtml
2. http://www.ncbi.nlm.nih.gov/blast/html/BLASThomehelp.html
3. http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html
4. http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html
5. http://www.psc.edu./biomed/training/tutorials/sequence/db/index.html
6. References:
[1] Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. "Basic local alignment search tool" Journal of Molecular Biology. 215: 403 - 410 The BLAST algorithm
[2] Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs" Nucleic Acids Research. 25: 3389 - 3402.

omniBLAST

OmniBLAST will perform a recursive BLAST search on a set of protein databases (BLASTP or BLASTX, depending on the query sequence) or nucleotide databases (BLASTN and TBLASTX or TBLASTN) available at the Sanger Institute and return a list of the best five HSP for each database. If there are any HSP you can click on Full Search to see the complete BLAST output.

The datasets:

T. brucei GeneDB predicted genes (coding sequences)	DNA sequence of all predicted coding sequences in the T. brucei strain 927 genome as well as those predicted in the 3 strain 427, variant 221a expression site BACs.
T. brucei GeneDB predicted proteins	Predicted protein sequence of all coding sequences in the T. brucei strain 927 genome as well as those predicted in the 3 strain 427, variant 221a expression site BACs.
T. brucei contigs (DNA)	The sequences of all contigs accessible through GeneDB.
chromosome IX reads
chromosome IX contigs
chromosome X reads
chromosome X contigs
chromosome XI reads
chromosome XI contigs
GSS/EST clusters	The above GSSs clustered with ESTs. ESTs listing Trypanosoma brucei as organism (i.e. this will include ESTs from various subspecies and strains) were retrieved from public sequence databases for this analysis (see here for more information).
EMBL	Last updated on June 2003 and containing all T. brucei sequences submitted to public databases. This does also include the TIGR "sequencing in progress" BAC clones, and therefore allows searching of all the submitted TIGR data.
African trypanosome Uniprot data
T. brucei telomere test reads	Reads generated from the 427 and 927 pilot telomere sequencing project

Alternative BLAST servers

Ultimately, the goal is to be able to search all T. brucei data at one site and we are working in conjunction with TIGR to achieve this. However, in the meantime you could also try the following BLAST servers:

Parasite BLAST server at the EBI	This BLAST server is updated on a monthly basis from EMBL and GenBank.
T. brucei BLAST server at TIGR	Similarity searches against sequence reads
	Similarity searches against BAC end sequences
	Similarity searches against clustered ESTs
NCBI BLAST server	This BLAST server includes sequences submitted to public databases and offers a variety of alignment tools.

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