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COMER web server for protein analysis by homology

  1. Enter your sequence, MSA, and/or profile queries below (use the line "//" to separate individual queries). (?)

    A query can represent a sequence, plain or in FASTA format, an MSA in aligned FASTA, STOCKHOLM, or A3M format, or a COMER2 profile (max 5 MB).

  2. Select target databases.
  3. Tune sequence search options to build informative MSAs for the queries.
  4. Click "Submit".
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Upload queries as an input text file (max 50 MB).

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When the input is a set of sequences in FASTA or aligned FASTA format, instruct the server to consider each sequence (gaps ignored) as a separate single sequence query (as if they were separated by "//").

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Use the COTHER method to search profile database(s) selected below with the input queries.

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Select one or more profile databases to search using COMER2 (multiple selection: Ctrl key + Mouse's left-click).

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Select one or more profile databases to search using COTHER (multiple selection: Ctrl key + Mouse's left-click).

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Specify a statistical significance threshold. Hits with an E-value greater than this value will not be displayed. (Possible real values: [0,100]).

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Specify a maximum number of hits to display on output (max 2000).

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Optionally, provide an e-mail address which will then be used to send a notification upon job completion.

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Optionally, provide a custom job description.

Sequence search options

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Perform additional sequence search with the sequence and MSA queries using HHblits to build informative MSAs.

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Select an HHsuite database to search using HHblits.

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Specify a number of HHblits iterations (max 4).

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Specify a statistical significance threshold for matches found by HHblits. Sequences identified with an E-value greater than this value will be ignored. (Possible real values: [0,1]).

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Perform additional sequence search with the sequence and MSA queries using HMMER to build informative MSAs (can be used along with HHblits).

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Select a sequence database to search using HMMER.

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Specify a number of HMMER iterations (max 4).

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Specify a statistical significance threshold for matches found by HMMER. Sequences identified with an E-value greater than this value will be ignored. (Possible real values: [0,1]).

Advanced options for COMER

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Apply low-complexity region filtering to the sequences of a final MSA from which a COMER2/COTHER profile is constructed. Profile construction can fail if all sequences in an MSA are low-complexity sequences.

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Specify a weight for the scoring term from Bayesian modeling of substitution probabilities. (Possible real values: (0,1)).

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Specify a weight for the term for scoring normally distributed context vectors. (Possible real values: [0,1)).

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Specify a weight for the term for scoring the similarity of secondary structures. 0 disables secondary structure scoring. (Possible real values: [0,1)).

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Specify a method for estimating the statistical significance of profile-profile alignments. 0, Statistical significance depends on alignment score and profile lengths; 1, Statistical significance depends on alignment score, profile attributes, and compositional similarity; 2, Same as model 1 but regards the amount of data used in simulations.

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Realign profile-profile alignments by a maximum a posteriori algorithm.

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Specify a posterior probability threshold for expected alignment accuracy of realigned pair of profiles. Alignment extension stops when the expected alignment accuracy drops below this value. 0 implies semi-global alignment. Threshold values tending to 1 shorten alignments. (Possible real values: [0,1)).

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Specify a weight for scoring inter-residue distance distribution match. Higher values emphasize the similarity of structural features, i.e., distance map similarity. (Possible real values: [0,1))