WU-BLAST (Parasite Genomes Databases)

Introduction

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

Databases

Database

Database Name Description Abbreviation
Nematoda nem
Filarial fil
B.malayi brugia
O.volvulus oncv
Apicomplexa apicom
Plasmodium plas
P.falciparum plasf
T.gondii toxo
C.parvum crypto
Eimeria eimeria
Kinetoplastids kineto
Schistosoma schisto
Schisto unique schunq
S.mansoni mansoni
S.japonicum jap
Cerc unique cercunq
Jap unique japunq
entamoeba entamoeba
bgESTnr bgESTnr

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.

Sequence Type

Indicates if the sequence is protein or DNA/RNA.

Type Abbreviation
PROTEIN protein
DNA/RNA dna

Default value is: DNA/RNA [dna]

Step 3 - Parameters

Program

The BLAST program to be used for the Sequence Similarity Search.

Program Name Description Abbreviation
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

Matrix

The comparison matrix to be used to score alignments when searching the database

Matrix Name Abbreviation
internal (default) internal
identity identity
PuPy pupy
BLOSUM62 blosum62
BLOSUM45 blosum45
BLOSUM50 blosum50
BLOSUM80 blosum80
BLOSUM90 blosum90
PAM30 pam30
PAM70 pam70
PAM250 pam250

Default value is: internal (default) [internal]

Additional information

Expectation Threshold

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) [10]

Filter

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.

Name Desciption Value
none No filtering of the query sequence. none
dust Mask simple repeats in DNA/RNA sequences dust

View Filter

When set to "yes" the query sequence used for the search, post filtering, is shown in the output file.

Sensitivity

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.

Sensitivity Actual Setting Value
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
normal N/A normal
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

Strand

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.

Scores

Maximum number of match score summaries reported in the result output.

Default value is: 50 (default) [50]

Alignments

Maximum number of match alignments reported in the result output.

Default value is: 50 (default) [50]

Sort

Sorts the scores in the score list of the output file.

Default value is: pvalue

Stats

The statistical model to use for assessing the significance of the hits found

Default value is: sump

topcomboN

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

Alignment Views

Formating for the alignments

Name Description Value
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 [1]

Translation Table

Query Genetic code to use in translation

Name Value
N/A -1
Standard 1
Vertebrate Mitochondrial 2
Yeast Mitochondrial 3
Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma 4
Invertebrate Mitochondrial 5
Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear 6
Echinoderm Mitochondrial 9
Euplotid Nuclear 10
Bacterial and Plant Plastid 11
Alternative Yeast Nuclear 12
Ascidian Mitochondrial 13
Flatworm Mitochondrial 14
Blepharisma Macronuclear 15
Chlorophycean Mitochondrial 16
Trematode Mitochondrial 21
Scenedesmus obliquus mitochondrial 22
Thraustochytrium mitochondrial 23
Codon2004 1001

Default value is: Standard [1]

Step 4 - Submission

Job title

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.

Email Notification

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.

Email Address

If email notification is requested, then a valid Internet email address in the form joe@example.org 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).

References

WU-Blast2 server at the European Bioinformatics Institute.
(2003 Jul 01) Nucleic acids research 31 (13) :3795-8
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
(1997 Sep 01) Nucleic acids research 25 (17) :3389-402
Basic local alignment search tool.
(1990 Oct 05) Journal of molecular biology 215 (3) :403-10
A new bioinformatics analysis tools framework at EMBL-EBI.
(2010 Jul) Nucleic acids research 38 (Web Server issue) :W695-9
Analysis Tool Web Services from the EMBL-EBI.
(2013 Jul) Nucleic acids research 41 (Web Server issue) :W597-600