tblastx: search translated nucleotide databases using a translated nucleotide query

BLAST Basic Local Alignment Search Tool

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TBLASTX search translated nucleotide databases using a translated nucleotide query. more...

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Enter Query Sequence

Enter accession number, gi, or FASTA sequence [?] Clear

Query sequence(s) to be used for a BLAST search should be pasted in the text area. It automatically determines the format or the input. To allow this feature there are certain conventions required with regard to the input of identifiers. more...

Query subrange [?]

From
To

Enter coordinates for a subrange of the query sequence. The BLAST search will apply only to the residues in the range. Sequence coordinates are from 1 to the sequence length.The range includes the residue at the To coordinate. more...

Or, upload file

[?]

Use the browse button to upload a file from your local disk. The file may contain a single sequence or a list of sequences. The data may be either a list of database accession numbers, NCBI gi numbers, or sequences in FASTA format.

Genetic code

Job Title

Enter a descriptive title for your BLAST search [?]

This title appears on all BLAST results and saved searches.

Blast 2 sequences [?]

To get the CDS annotation in the output, use only the NCBI accession or gi number for either the query or subject. Reformat the results and check 'CDS feature' to display that annotation.

Enter Subject Sequence

Enter accession number, gi, or FASTA sequence [?] Clear

Subject sequence(s) to be used for a BLAST search should be pasted in the text area. It automatically determines the format or the input. To allow this feature there are certain conventions required with regard to the input of identifiers. more...

Subject subrange [?]

From
To

Enter coordinates for a subrange of the subject sequence. The BLAST search will apply only to the residues in the range. Sequence coordinates are from 1 to the sequence length.The range includes the residue at the To coordinate. more...

Or, upload file

[?]

Choose Search Set

Database

Human genomic + transcript Mouse genomic + transcript Others (nr etc.):

[?]

Select the sequence database to run searches against. No BLAST database contains all the sequences at NCBI. BLAST databases are organized by informational content (nr, RefSeq, etc.) or by sequencing technique (WGS, EST, etc.). more...

Organism
Optional

Enter organism common name, binomial, or tax id. Only 20 top taxa will be shown. [?]

Select from the list or choose “Custom” to enter the name of an organism. The search will be restricted to the sequences in the database which are from the organism selected.

Entrez Query
Optional

Enter an Entrez query to limit search [?]

You can use Entrez query syntax to search a subset of the selected BLAST database. This can be helpful to limit searches to molecule types, sequence lengths or to exclude organisms. more...

Program Selection Optimize for

Highly similar sequences (megablast)

More dissimilar sequences (discontiguous megablast)

Somewhat similar sequences (blastn)

Choose a BLAST algorithm [?]

Megablast is intended for comparing a query to closely related sequences and works best if the target percent identity is 95% or more but is very fast.
Discontiguous megablast uses an initial seed that ignores some bases (allowing mismatches) and is intended for cross-species comparisons.
BlastN is slow, but allows a word-size down to seven bases.

more...

Algorithm

blastp (protein-protein BLAST)

PSI-BLAST (Position-Specific Iterated BLAST)

PHI-BLAST (Pattern Hit Initiated BLAST)

Enter a PHI pattern [?]

Enter a PHI pattern to start the search. PHI-BLAST may perform better than simple pattern searching because it filters out false positives (pattern matches that are probably random and not indicative of homology).

Choose a BLAST algorithm [?]

BlastP simply compares a protein query to a protein database.
PSI-BLAST allows the user to build a PSSM (position-specific scoring matrix) using the results of the first BlastP run.)
PHI-BLAST performs the search but limits alignments to those that match a pattern in the query.

Search using Tblastx (Search translated nucleotide databases using a translated nucleotide query)
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Algorithm parameters Note: Parameter values that differ from the default are highlighted in yellow

General Parameters Max target sequences

Select the maximum number of aligned sequences to display [?]

Maximum number of aligned sequences to display (the actual number of alignments may be greater than this).

Short queries

Automatically adjust parameters for short input sequences [?]

Automatically adjust word size and other parameters to improve results for short queries.

Expect threshold

[?]

Expected number of chance matches in a random model. more...

Word size

[?]

The length of the seed that initiates an alignment. more...

Scoring Parameters Matrix

[?]

Assigns a score for aligning pairs of residues, and determines overall alignment score. more...

Match/Mismatch Scores

[?]

Reward and penalty for matching and mismatching bases. more...

Gap Costs

[?]

Cost to create and extend a gap in an alignment. more...

Compositional adjustments

[?]

Matrix adjustment method to compensate for amino acid composition of sequences. more...

Filters and Masking Filter

Low complexity regions [?]

Mask regions of low compositional complexity that may cause spurious or misleading results. more...

Species-specific repeats for: [?]

Mask repeat elements of the specified species that may lead to spurious or misleading results. more...

Mask

Mask for lookup table only [?]

Mask query while producing seeds used to scan database, but not for extensions. more...

Mask lower case letters [?]

Mask any letters that were lower-case in the FASTA input. more...

Discontiguous Word Options Template length

[?]

Total number of bases in a seed that ignores some positions. more...

Template type

[?]

Specifies which bases are ignored in scanning the database. more...

PSI/PHI BLAST

PSSM

PSSM is uploaded... Clear

Upload PSSM Optional

[?]

Upload a Position Specific Score Matrix (PSSM) that you previously downloaded from a PSI-BLAST iteration. You may search a different database than that used to generate the PSSM, but you must use the same query. more...

PSI-BLAST Threshold

[?]

Set the statistical significance threshold to include a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.

Search using Tblastx (Search translated nucleotide databases using a translated nucleotide query)
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