TSeq: Tripal Sequence Similarity Search

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Similarity Search Overview

Sequence similarity search is supported in TreeGenes against genes, TreeGenes UniGenes, proteins, and full genomes. Nucleotide searches are executed with BLAST (BLASTN) while protein or translated protein searches are executed with DIAMOND (BLASTX or BLASTP equivalent). DIAMOND will execute searches in a fraction of the time of BLAST at a similar sensitivity. Both packages accept similar input parameters and these can be modified below. You may upload FASTA formatted sequences or paste FASTA formatted sequences for searching. You can select from a list of pre-formatted DIAMOND and BLAST databases OR upload your own. This can be pre-formatted or provided in FASTA format and formatted for you.

Sequence Query Type

Protein

Nucleotide (coding or whole genome)

Database Search Type

Provide/load Query Sequence

Target/Database Selection

Protein

Gene

Genome

Protein (UniGene)

Gene (UniGene)

Protein (TSA)

Upload your own database/target

Provide/Select search database:

Select from an existing database

Upload a File

Type or paste manually

Raw target data

Target File

Advanced Options

E-value * Expected number of chance matches in a random model. This number should be give in a decimal format.

Target Coverage * Report only alignments above the given percentage of subject cover.

Query Coverage * Report only alignments above the given percentage of query cover.

Max Alignments The maximum number of target sequences per query to report alignments for.

Upon Submission, your search will enter the queue with either BLAST or Diamond as the engine. You will be given a link to view the progress and results of the job.

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Sequence Query Type

Provide/load Query Sequence

Target/Database Selection