Nocardia farcinica IFM 10152 Nucleotide BLAST
BLASTN programs search nucleotide databases using a nucleotide 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...

Help

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 Help

This title appears on all BLAST results and saved searches.

Help

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.

New columns added to the Description TableNew
Click 'Select Columns' or 'Manage Columns'.
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...

 
Help

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
Help

Database sequences non-default value

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

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.


Enter an Entrez query to limit search Help

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
Choose a BLAST algorithm Help
  • 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...

Help

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 Help
  • 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)
Note: Parameter values that differ from the default are highlighted in yellow and marked with sign