Introduction

You may search a wide range of sequence databases for sequences similar to your query sequence. Please select the type of query sequence, enter the query sequence, select the database to search, and click search. Optionally, you may change other parameters, including which of two very sensitive algorithms to use. If anybody else is running a search when you try to start a search, your search will be queued. You will be informed of when the search is estimated to be finished.

Query Type

Select whether the query is a sequence of amino acids (default), nucleotides, or nucleotides that should be translated into amino acid sequences in all six frames before searching.

Query Sequence

Enter one or more query sequences. Sequences can be entered directly as text, or uploaded in a file.
Accepted formats are: plain text (single sequence only), FASTA, EMBL/SWISSPROT and GenBank/GenPept.
Queries with a total length of more than 100,000 symbols are not accepted. Illegal symbols in the sequence will be ignored.

Database

Select the sequence database to be searched. Most of the available databases are public sequence databases that are updated weekly from the NCBI. If a nucleotide sequence database is selected and the query is an amino acid sequence (possibly translated), the database sequences will be translated into amino acid sequences in all six frames.

Algorithm

Choose between an accelerated version of the Smith-Waterman algorithm or the ParAlign algorithm (default), which is much faster but still almost as sensitive. The Smith-Waterman algorithm will usually be the best algorithm for extremely short queries (less than 10 amino acids).

Scoring System

Select the combination of score matrix and gap penalties to be used for scoring the alignments. If both the query and database are untranslated nucleotide sequences, a direct nucleotide comparison will be made using a nucleotide scoring system. Otherwise an amino acid sequence comparisons will be made.

Expect Range

Select the range of expect values (E-values) required for hits to be shown. Both a lower limit and an upper limit may be set. The upper limit (default 10) determines the statistical significance required by a hit, as expressed by an expectation value. The lower limit (default 0) can be set to exclude obvious hits that are very similar to the query. For very short queries an upper limit of 1000 or higher might be required to see any hits.

Max Hits

Select the maximum number of hits that are shown in the list of hits.

Max Alignments

Select the maximum number of hits that are shown with a full alignment and other information.

Max Sub-Alignments

Select the maximum number of non-overlapping alignments within the same sequence to show (default 1). There may exist several non-overlapping alignments of the query and a database sequence that have a significant score (as specified by the expect range). Selecting a higher value than default for this option can be used to display more than the first (highest scoring) one.

Query Strands

Select which strands of the query sequence to use: both strands (default), only the upper (forward, Watson) strand or only the lower (reverse complement, Crick) strand. If the query sequence is being translated into amino acid sequence during searching, only the three frames on the selected strand will be used. This option is ignored for amino acid queries.

Search by organisms

By selecting one or more of the check boxes, the search will be restricted to only those sequences in the database belonging to these organisms. The resulting e-values will be given as if the database only consisted of these sequences. If you do not select any of the boxes your search will not be restricted by organisms, but will run as normal.

Taxonomy identifier

By entering one or more taxonomy identifiers (taxid), the search will be restricted to only those sequences in the database belonging to these organisms. The resulting e-values will be given as if the database only consisted of these sequences. If left empty your search will not be restricted by organisms, but will run as normal. Taxid example: "9606" restricts to human sequences. A comma separated list like: "9606,10090" restricts to human and mouse sequences.

Misc.

Checking the checkbox opens up a new window that will contain the result once finished. Entering your email address will send you a notification by email when the result is finished. Your email address will not be stored on our servers.