Skip to content
Metazome release 2.0.4 24 metazoan proteomes 9 ancestral nodes DOE JGI and University of California
Metazome

Tools / Sequence search

BLAST a sequence

Place a protein or nucleotide sequence against a single organism genome or an ancestral node consensus set. Choose the target, set the program and parameters, then review the prepared job.

BLAST help
Job preparation only. This static edition validates the query and builds a job summary. It does not run the alignment in the browser. To run a public sequence search now, use NCBI BLAST.

Step 2

Describe the job

The form follows the options documented for the Metazome BLAST service. The summary below the form shows exactly what has been prepared.

Program
Query

Paste a protein or nucleotide sequence in FASTA format, with or without a header. The page validates the sequence and prepares a job summary.

The file is read in your browser and placed in the sequence box.

Algorithm parameters

Default is 11 for BLASTN and 3 for other programs.

Reference

BLAST options

The Metazome BLAST service implemented NCBI BLAST (v2.2.13) for sequence similarity searches of individual organism genomes and cluster consensus sequences defined at each node. The available options follow the standard NCBI options described below.

Allow gapped alignment
Permit gaps in the alignment between the query and target sequence.
Comparison matrix
The scoring matrix that determines the cost of each possible residue mismatch between the query and target sequence.
Word length
The minimum number of consecutive residues that must match identically between the query and target sequence to seed an alignment.
E threshold
The maximum expectation value of retained alignments.
Number of alignments to show
How many top scoring alignments should be displayed in the result set.
Filter options
Whether to remove low complexity regions from the query sequence, using DUST for BLASTN searches and SEG for all other programs.
Include singletons
For node consensus searches, choose whether to include clusters of size one in the target database.

For the full description of targets, results, and composite clusters, see the BLAST help section.