New job submissions
Using the tools provided on this page, you can create a profile or paste in a pre-created profile, then compare the profile
with profiles of more than 350,000 proteins from 89 different genomes.
You can create a phylogenetic profile by submitting an amino acid sequence (or its GenBank Identifier), which can then be
compared with profiles that are stored in our database.
If you already have a profile, you can search for matching profiles by choosing BLAST Evalue scores for each position,
and combining these values with operators, such as 'greater than' or 'equal to', which will present the value accordingly
for comparison. Profiles can be searched for by specifying groups (for instance, you can choose presence in all Archaea,
and any value for the rest of the genomes), or by specifying values for individual genomes. To avoid a certain numbness of
the mind (if you don't want to select an operator and value for each genome), you can even paste in a preconstructed profile
(see instructions for the format).
Please note that your results are stored on our system for a period of 24 hrs from the time a Job ID
was assigned to you. This Job ID can be used to retrieve your results. Currently, you cannot retrieve profiles that you searched
for by specifying Evalues and operators, but this feature will be available shortly.
For help, please write to marcotte AT icmb dot utexas.edu
I want to search for profiles, and I have a profile that I can paste in
Required format:
Single line with 89 space separated values (eg: 1e-1 1e-2 1e-3 ... 1e-89), where an Evalue >= 1.00, 'N' or
missing values indicate absence from the designated genome.
Note:
- BLAST E-values become more significant as they decrease.
- Please make sure that each value corresponds to the appropriate genome, based on this
genome list.
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I want to search for profiles, and define my own values and operators
You can search for profiles with Evalues and operators either based on phylogenetic groups, or on individual genomes.
Operators you can use (to define BLAST Evalue boundaries):
> Greater than | < Less than
= Equal to | * Any
! Is Not (!=) |
Operators take precedence over Evalues (i.e., Evalues are accepted only if the operator is not '*').
BLAST E-values become more significant as they decrease.
So, to indicate the presence of a gene, use the '<' (less than) operator.
Search for a profile by specifying operators and Evalues for individual genomes
Note: Admittedly, this is one of the most difficult to use, but also one of the most powerful tools in PLEX repertoire.
Please make a careful note of what each of the operators signifies, and the all the possible combinations of
the results that can be obtained. A few tips follow:
- BLAST E-values become more significant as they decrease. Therefore, in most instances, using the '<'
operator would capture the desired E-value, and all subsequent lower E-values for a given instance in a
genome.
- When constructing profiles directly from BLAST results, please note that PLEX uses the highest hit and
its statistics in each genome to indicate presence. Therefore, only the topmost hit for any genome is
relevant.
- If the default '*' (any) operator is left unchanged, it will not exclude presence of your query in any
genome, rather, it will select any observed E-value. This means that if the profile you desire is not very
specific, the results will contain all observed combinations, along with the desired answer!
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Copyright © 2002 - 2004, Shailesh Date and Edward Marcotte. The protein link explorer data and
server is the property of the University of Texas, and cannot be used for commercial purposes without
written permission of Edward Marcotte and the University of Texas. It is forbidden to redistribute,
derivatize, or encapsulate the protein link explorer data or server in another database without permission.
Sale of information derived from it, whether directly or in revised form, is forbidden except by permission of
UT and Edward Marcotte. All copies or mirrors of the protein link explorer must carry this notice.
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