Microbial Protein BLAST
BLASTP programs search protein databases using a protein query. more...
Enter Query Sequence
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...

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...

 
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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.


Enter a descriptive title for your BLAST search [?]

This title appears on all BLAST results and saved searches.

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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.

BLAST has New Default Parameters and Search Limits.New
Enter Subject Sequence
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...

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...

 
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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.

Choose Search Set
Microbial proteins [?]

The microbial proteins are the bacteria and archeae subset from nr.

♦Database sequences non-default value
Add organism

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

Start typing in the text box, then select your taxid. Use the "plus" button to add another organism or group, and the "exclude" checkbox to narrow the subset. The search will be restricted to the sequences in the database that correspond to your subset.

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Each non-redundant RefSeq proteins represent a collection of identical proteins and provides information about the protein sequence and name with links to information about genomic context. More information is available at https://www.ncbi.nlm.nih.gov/news/06-11-2013-wp-refseqs/

Program Selection
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...

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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 [?]
  • 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 Blastp (protein-protein BLAST)
Algorithm parameters Note: Parameter values that differ from the default are highlighted in yellow and marked with ♦ sign
General Parameters
♦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).

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

♦Expect threshold non-default value [?]

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

♦Word size non-default value [?]

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

♦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 non-default value [?]

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


♦Match/Mismatch Scores non-default value [?]

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

♦Gap Costs non-default value [?]

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

♦Compositional adjustments non-default value [?]

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

Filters and Masking
♦Low complexity regions filter non-default value [?]

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

♦Species-specific repeats filter non-default value [?]

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

♦Mask for lookup table only non-default value [?]

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

♦Mask lower case letters non-default value [?]

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

Discontiguous Word Options
♦Template length non-default value [?]

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

♦Template type non-default value [?]

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

PSI/PHI/DELTA BLAST
♦PSSM non-default value
PSSM is uploaded... Clear
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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...

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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 non-default value [?]

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

♦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 Blastp (protein-protein BLAST)