Sequence Input

Sequences for comparison can be either pasted into the 'Paste Sequences' box, or a file containing the sequences can be uploaded
The sequences should be in fasta, EMBL or Genbank formats
Multiple sequences can be uploaded or pasted in the same file

Set Job Name

You can set the name of this job to help identify it in future.
The job name can contain letters, spaces or numbers only.

Select the database to search here

The Blumeria graminis genome is available to search as supercontigs and contigs, either as a filtered set which excludes supercontigs less than 2 kb in size, or greater than 70% repetitive, of an unfiltered set of all supercontigs/contigs. The Gene predictions were produced using Eugene. EST sequences are available as individual libraries, or as a database of clustered unigenes.

Program Selection

A number of different BLAST programs are available which vary in their sensitivity.

• For extremely closely-related sequences (i.e. from other Blumeria strains), try using megablast. This is the best option to identify identical sequences
• Discontiguous megablast allows a number of mismatches in the intial word match, so is appropriate for slightly less similar (i.e. cross-species) searches
• BlastN is less sensitive again, and is slower, but allows a much smaller initial word size to be used
• For sequences from considerably divergent organisms, try TblastX, which carries out a protein level comparison between a six-frame translation of the query sequence and a six-frame translation of the database. This is much slower and will tend to produce a large number of overlapping HSPs in areas of similarity. Only use this if the less sensitive methods have failed to identify sequences similar to your query. You can also search protein sequences against translations of the DNA databases using TBlastN

Max Target Sequences

Selects the maximum number of alignments to display

Expect Value

Statistical significance threshold for reporting matches against database sequences
Lower expect thresholds result in less matches occuring by chance being reported

Wordsize

Blast starts by looking generating a seed alignment for a match of a given length
Reducing the wordsize increases the sensitivity of the search, but increases the runtime.

Template Length

Discontiguous megablast allows for a certain number of mistmatches in the initial seed alignment. This parameter determines the number of matches required in this seed alignment.. See the NCBI documentation for further details.

Template Type

Defines which bases may be ignored during the seed alignment. See the NCBI documentation for further details.

Scoring Matrix

Determines matrix used for assigning scores for matching/similar amino acids. For further information see the NCBI documentation.

Match Scores

Defines the "reward" and "penalty" values used for scoring nucleotide alignments

Gap Costs

Costs to open and extend a gap. Megablast also has a linear setting, where the match/mismatch scores are used the match/mismatch scores are used.

Filtering

Masks low-complexity regions of the sequence which may produce erroneous results.