COG Database Query Page
Similarity search in COG DataBase: function and COG category guess (*)
Similarity searches are performed with GAPPED-BLAST (BLAST 2.2.3 [May-13-2002] NCBI, Altschul et al., 1997, Nucleic Acids Res. 25:3389-3402)
For cogs overview:
Tatusov, R.L., Koonin, E.V., and Lipman, D.J. (1997). Science 278: 631-637.
Tatusov, et al. (2001). Nucleic Acids Res 29: 22-28.
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Enter your sequence (fasta) or a gene number (eg: PAB0255) here:
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Search domain :
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Display full alignements in graphics
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(*) A query sequence is BLASTed vs . the COG database, then results from this search are compiled according to
several criteria (see below in red) in order to give an estimation - a guess- of the most probable category and COG
number of the query. Please take into account the following :
- True fitting of proteins in the COG database are made by COGNITOR program and E. Koonin group members
- As this procedure is completely automatic, it is important to discard potentially wrong assignments by a careful
examination of sequence alignments.
- Results STATUS legend :
- good = match length > 50 % of query sequence length, number of best COG matches > 1/4 total number of matched COGs
suspect: MH = multiple hits in COG database, number of best COG matches < 1/4 total number of matched COGs
suspect: LH = Less than 3 Hits in COG database
suspect: HSP = match length <= 40 % of orf length
suspect: Pn = expect value (Pn) for best match is near cut off value (1e-07)
suspect: %id = % identity of best hits is less than 25% over matched length
normal = all the rest
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Blast version 2 Advanced Options
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Expectation value (E)
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[Real]
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Matrix
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Filter query sequence
(DUST with blastn, SEG with others)
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True False
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Perform gapped alignment
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True False
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Cost to open a gap
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[Integer]
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One-line descriptions (V)
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[Integer]
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Cost to extend a gap
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[Integer]
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Alignments to show (B)
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[Integer]
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X dropoff value
for gapped alignment (in bits)
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[Integer]
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Threshold for extending hits
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[Integer]
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