Paste a Sequence | Upload a File | Accession Search
Click the example link to add a sequence to the search box. The form requires a single sequence protein in FASTA format, with or without a header line. To search multiple sequences, (up to 500) click 'Upload a file'.
Choose one of the following target databases for your query to be searched against. The databases vary substantially in size and the amount of functional annotation.
Select specific taxonomy groupings from the target sequence database.
Enter a taxonomic name or NCBI taxid
There are two different ways of controlling which target sequences match your query. E-value:Control both significant and reporting thresholds for the entire sequence and each hit, 10≥x>0. May be entered with scientific notation. Bit score:Control both significant and reporting thresholds for the entire sequence and each hit, x>0.
This section allows the selection of columns and the number of rows that are displayed in the results table. You can also customise the table after the search has been performed.
Select Visible Columns
Choose the different columns to be displayed in the table. The more columns added, the wider the table, which may make the browser window scroll horizontally.
Rows Per Page
Select the number of rows in the table. If the total number of results exceeds this, then results will be paginated. The larger the number, the more work your browser has to do in order to render the table. Over 1000 rows you are likely to get 'slow JavaScript' warnings from your browser.
open:sets the gap open probability. The default is 0.02. Values must be ≥ 0 and < 0.5.extend:sets the gap extend probability. The default is 0.4. Values must be ≥ 0 and < 1. matrix:the amino acid substitution matrix used for constructing the probability model. The default is BLOSUM62.
Under some circumstances, hits can be lost due to the fact a sequence, or regions of a sequence, are omitted due to bias composition. You can turn this filter off, but it will slow down your searches.
HMMER