PLEX Help/FAQs

Query:
Amino acid sequence input by the user.

Raw Blast Results:
Sequence comparison results displayed as calculated by the BLAST algorithm. For more information on BLAST, see http://www.ncbi.nlm.nih.gov/BLAST/.

Blast Results in Apropos Format:
A condensed form of the sequence comparison results generated by the BLAST. Information relevent to further analysis on APROPOS.is only displayed.

Phylogenetic profile Information:
The presence or absence of a protein in a genome is assayed using sequence comparison results obtained by BLAST. Expect (e) values obtained by BLAST searches are then used to construct a phylogenetic profile vector for each protein. These profile vectors can then be compared to profile vectors of other proteins. Similarity between phylogenetic profiles of proteins have been shown to correlate with similarity in function. For more information on phylogenetic profiles, see:

1. Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. & Eisenberg, D.  A Combined Algorithm for Genome-Wide Prediction of Protein Function. Nature 402, 83-86 (1999). 
2. Marcotte, E. M., Pellegrini, M., Ng, H.-L., Rice, D. W., Yeates, T. O. & Eisenberg, D.  Detecting Protein Function & Protein-Protein Interactions from Genome Sequences.   Science  285, 751-753(1999).
3. Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. & Yeates, T. O.: Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.. Proc. Natl. Acad. Sci. 96, 4285-4288 (1999).

Phylogenetic Profile:
See Phylogenetic Profile Information.

Number genomes in phylo profile vector:
The number of genomes that were scanned for the presence or absence of the query protein. The current number of genomes that we have on our servers is 57+2(A.thaliana Chr1 north and south arms are treated as separate for sake of simplicity).

Profile comparison:
See Phylogenetic Profile Information.

Cutoff Value
Mutual Information (MI) values above this cutoff value are displayed. In reality, a query profile compared with a set of randomized profiles rarely score above 0.5 (Date and Marcotte, manuscript in preparation, link will be displayed here for information).

Genome Selection:
The user can select a particular genome against which the query protein profile can be compared.

Omit hits to homologs/self:
This is a logical step that is recommended. Hits to homologs and self will always result in high mutual information values. However, in some cases, this box may be left unchecked, if for instance, a validation or comparion of the results obtained has to be carried out.

Analysing the results:
This section is incomplete. Our apologies.