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2Can Support Portal - Protein and Proteomic AnalysisBLAST similarity search <<< 11/12 >>>
Comparison of WU-BLAST2 and NCBI-BLAST2 results
Results of the WU-BLAST2 search
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Results of the NCBI-BLAST2 search
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We can see that under these conditions, both BLAST programs return the same results, but however they provide slightly different options for "tweaking" the results. These are described below.
- With NCBI-BLAST2 you have the option of 6 ways to display the alignments (pairwise, M/S with identities, M/S without identities, Flat Query-anchored with identities , Flat Query-anchored without identities ), with WU-BLAST2 you can only display pairwise alignments. More about align views
- With WU-BLAST2 you can sort results via different criteria (p-value, count, high score, total score), but not NCBI-BLAST2 where the scores are only sorted via bit score. More about sort criteria
- With WU-BLAST2 you can adjust the sensitivity option, which means you can perform a search with different levels of sensitivities, so you can perform a quick search with very low sensitivity in around 30 seconds, or do a more stringent search, which will take several minutes. More about sensitivity. NCBI-BLAST2 has a lower sensitivity setting as default options and is therefore a little faster than WU-BLAST2 with default settings.
- With NCBI-BLAST2 you can adjust gapopen/extension penalties, these are fixed values with WU-BLAST2. More about gaps
- With WU-BLAST2 you have a choice of seg, gnu, seg + gnu filters for a protein BLAST, NCBI-BLAST2 only offers a dust filter as with WU-BLAST2, which is used for DNA vs DNA searches.
- NCBI's BLAST has hardcoded matrices and gaps to internal tables in
the code. Although the user can change the matrix to use for comparision it
is difficult, if not impossible, to guess which are the correct gap values
to use. In this respect WU-BLAST is easier to use and much more forgiving,
allowing the user more freedom to detect very remote relationships without
sacrificing specificity.
We will next look at some useful references >>>
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Smallest Sum High Probability Sequences producing High-scoring Segment Pairs: Score P(N) N UNIPROT:AAC2_MOUSE Q9JI91 Alpha-actinin 2 (Alpha actinin sk... 4653 0. 1 UNIPROT:AAK64510 AAK64510 Actinin alpha 2. 4604 0. 1 UNIPROT:AAC2_HUMAN P35609 Alpha-actinin 2 (Alpha actinin sk... 4581 0. 1 UNIPROT:AAC2_CHICK P20111 Alpha-actinin 2 (Alpha actinin sk... 4434 0. 1 UNIPROT:Q8R4I6 Q8R4I6 Skeletal muscle-specific alpha-actini... 3821 0. 1 UNIPROT:AAC3_MOUSE O88990 Alpha-actinin 3 (Alpha actinin sk... 3815 0. 1 UNIPROT:AAM26632 AAM26632 Truncated alpha-actinin. 3805 0. 1 UNIPROT:AAC3_HUMAN Q08043 Alpha-actinin 3 (Alpha actinin sk... 3790 0. 1 UNIPROT:AAC1_CHICK P05094 Alpha-actinin 1 (Alpha-actinin cy... 3750 0. 1 UNIPROT:AAC1_RAT Q9Z1P2 Alpha-actinin 1 (Alpha-actinin cyto... 3745 0. 1