WU-BLAST (Parasite Genomes Databases)
WU-BLAST stands for Washington University Basic Local Alignment Search Tool. The emphasis of this tool is to find regions of sequence similarity or homology quickly, with minimum loss of sensitivity. This will yield functional and evolutionary clues about the structure and function of your novel sequence. Dr Warren Gish at Washington University released this first "gapped" version of BLAST allowing for gapped alignments and statistics.
How to use this tool
Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.
Each tool has at least 2 steps, but most of them have more:
- The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
- In the following steps, the user has the possibility to change the default tool parameters
- And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server
Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.
Step 1 - Database
Default value is: Nematoda [nem]
Step 2 - Sequence
Sequence Input Window
The query sequence can be entered directly into this form. The sequence can be be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot format. A partially formatted sequence is not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present. There is a limit of 1MB for the sequence entry.
Sequence File Upload
A file containing a valid sequence in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot) can be used as input for the sequence similarity search. Word processor files may yield unpredictable results as hidden/control characters may be present. It is best to save files with the Unix format option to avoid hidden Windows characters. There is a limit of 1MB for the sequence entry.
Indicates if the sequence is protein or DNA/RNA.
Default value is: DNA/RNA [dna]
Step 3 - Parameters
The BLAST program to be used for the Sequence Similarity Search.
|blastn||Compares a nucleotide sequence (DNA/RNA) to a nucleotide sequence database||blastn|
|tblastx||Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Please note that TBLASTX is extremely slow and cpu-intensive.||tblastx|
|tblastn||Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames.||tblastn|
Default value is: blastn
The comparison matrix to be used to score alignments when searching the database
Default value is: internal (default) [internal]
- Additional information
Limits the number of scores and alignments reported based on the expectation value. This is the maximum number of times the match is expected to occur by chance.
Default value is: 10 (default) 
Filter regions of low sequence complexity. This can avoid issues with low complexity sequences where matches are found due to composition rather than meaningful sequence similarity. However in some cases filtering also masks regions of interest and so should be used with caution.
|none||No filtering of the query sequence.||none|
|dust||Mask simple repeats in DNA/RNA sequences||dust|
When set to "yes" the query sequence used for the search, post filtering, is shown in the output file.
Increasing the sensitivity will increase the length of the search (longer execution times + more memory required), but increase the specificity of the results. A decrease will significantly speed up the search but decrease the sensitivity of the results.
|very low||blastx/blastp: "W=5 T=1000 wink=2 hitdist=30"; blastn: "W=14 M=1 N=-3 Q=3 R=3 wink=2 hitdist=30"; tblastn/tblastx: "W=14 Q=3 R=3 wink=2 hitdist=30"||vlow|
|low||blastx/blastp: "T=1000 hitdist=40"; blastn: "W=12 M=1 N=-3 Q=3 R=3 hitdist=40"; tblastn/tblastx: "W=12 Q=3 R=3 hitdist=40"||low|
|medium||blastx/blastp: "hitdist=40"; blastn: "M=1 N=-3 Q=3 R=3"; tblastn/tblastx: "Q=3 R=3"||medium|
|high||blastx/blastp: "hspmax=0"; blastn: "W=9 gapW=24 hspmax=0"; tblastn/tblastx: "W=9 gapW=24 hspmax=0"||high|
Default value is: normal
For nucleotide sequences specify the sequence strand to be used for the search. By default both upper (provided) and lower (reverse complement of provided) strands are used, for single stranded sequences searching with only the upper or lower strand may provide better results.
Maximum number of match score summaries reported in the result output.
Default value is: 50 (default) 
Maximum number of match alignments reported in the result output.
Default value is: 50 (default) 
Sorts the scores in the score list of the output file.
Default value is: pvalue
The statistical model to use for assessing the significance of the hits found
Default value is: sump
Topcombo processing causes consistent sets of HSPs to be reported, such that any given HSP is allowed to be a member of just one set. Often, one wishes to see just the best set of consistent HSPs without any other "contaminants" in the output. This would be topcomboN=1.
Default value is: 1
Formating for the alignments
|pairwise||The query and match are output as a pairwsie alignment with a consensus line between the two sequences. In the consensus the match states are represented as: identical match as the base/residue, similarity as a '+' and missmatch as a space.||1|
|BLASTXML||Output NCBI BLAST XML instead of a plain text report.||7|
Default value is: pairwise 
Query Genetic code to use in translation
|Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma||4|
|Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear||6|
|Bacterial and Plant Plastid||11|
|Alternative Yeast Nuclear||12|
|Scenedesmus obliquus mitochondrial||22|
Default value is: Standard 
Step 4 - Submission
It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.
Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.
If email notification is requested, then a valid Internet email address in the form email@example.com must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).