Nucleotide BLAST: Align two or more sequences using BLAST

Align Sequences Nucleotide BLAST

BLASTN programs search nucleotide subjects using a nucleotide query. more...

Enter Query Sequence

Enter accession number(s), gi(s), or FASTA sequence(s) Clear

Enter query sequence(s) in the text area. It automatically determines the format of the input. To allow this feature, certain conventions are required with regard to the input of identifiers. more...

Query subrange

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...

Query subrangeFrom
Query subrangeTo

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.

Align two or more sequences

Enter one or more queries in the top text box and one or more subject sequences in the lower text box. Then use the BLAST button at the bottom of the page to align your 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(s), gi(s), or FASTA sequence(s) 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

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...

Subject subrangeFrom
Subject subrangeTo

Or, upload file

Program Selection Optimize for

Optimize for Highly similar sequences (megablast)

Optimize for More dissimilar sequences (discontiguous megablast)

Optimize for 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

Algorithm Quick BLASTP (Accelerated protein-protein BLAST)

Algorithm blastp (protein-protein BLAST)

Algorithm PSI-BLAST (Position-Specific Iterated BLAST)

Algorithm 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).

Algorithm DELTA-BLAST (Domain Enhanced Lookup Time Accelerated BLAST)

Choose a BLAST algorithm

QuickBLASTP is an accelerated version of BLASTP that is very fast and works best if the target percent identity is 50% or more.
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.
DELTA-BLAST constructs a PSSM using the results of a Conserved Domain Database search and searches a sequence database.

Search using Megablast (Optimize for highly similar sequences)
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Note: Parameter values that differ from the default are highlighted in yellow and marked with ♦ sign Algorithm parameters

General Parameters Max target sequences

♦Max target sequences non-default value
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

♦Expect threshold non-default value

Expected number of chance matches in a random model. more... Expect value tutorial

Word size

♦Word size non-default value

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

Max matches in a query range

♦Max matches in a query range non-default value

Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query. The algorithm is based upon //www.ncbi.nlm.nih.gov/pubmed/10890403

Scoring Parameters Matrix

♦Matrix non-default value

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

Match/Mismatch Scores

♦Match/Mismatch Scores non-default value

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

Gap Costs

♦Gap Costs non-default value

Cost to create and extend a gap in an alignment. Linear costs are available only with megablast and are determined by the match/mismatch scores. more...

Compositional adjustments

♦Compositional adjustments non-default value

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

Filters and Masking Filter

♦Low complexity regions filter non-default value Low complexity regions filter

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

♦Species-specific repeats filter non-default value Species-specific repeats filter for:

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

Mask

♦Mask for lookup table only non-default value Mask for lookup table only

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

♦Mask lower case letters non-default value Mask lower case letters

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

Discontiguous Word Options Template length

♦Template length non-default value

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

Template type

♦Template type non-default value

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

PSI/PHI/DELTA BLAST

PSSM ♦PSSM non-default value

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.

DELTA-BLAST Threshold

♦DELTA-BLAST Threshold non-default value

Set the statistical significance threshold to include a domain in the model used by DELTA-BLAST to create the PSSM

Pseudocount

♦Pseudocount non-default value

Pseduocount parameter. If zero is specified, then the parameter is automatically determined through a minimum length description principle (PMID 19088134). A value of 30 is suggested in order to obtain the approximate behavior before the minimum length principle was implemented.

Search using Megablast (Optimize for highly similar sequences)
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