WU-BLAST (Nucleotide 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
ENA Sequence (formerly EMBL-Bank) ENA Sequence (formerly EMBL-Bank) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications.
ENA Sequence Release The quarterly release of the ENA Sequence em_rel
ENA Sequence Environmental Sequences from Environmental Samples. em_rel_env
ENA Sequence EST Environmental em_rel_est_env
ENA Sequence GSS Environmental em_rel_gss_env
ENA Sequence HTC Environmental em_rel_htc_env
ENA Sequence HTG Environmental em_rel_htg_env
ENA Sequence Patent Environmental em_rel_pat_env
ENA Sequence Standard Environmental em_rel_std_env
ENA Sequence TSA Environmental em_rel_tsa_env
ENA Sequence Fungi Sequences from Fungi. em_rel_fun
ENA Sequence EST Fungi em_rel_est_fun
ENA Sequence GSS Fungi em_rel_gss_fun
ENA Sequence HTC Fungi em_rel_htc_fun
ENA Sequence HTG Fungi em_rel_htg_fun
ENA Sequence Patent Fungi em_rel_pat_fun
ENA Sequence Standard Fungi em_rel_std_fun
ENA Sequence STS Fungi em_rel_sts_fun
ENA Sequence TSA Fungi em_rel_tsa_fun
ENA Sequence Human Sequences from Human. em_rel_hum
ENA Sequence EST Human em_rel_est_hum
ENA Sequence GSS Human em_rel_gss_hum
ENA Sequence HTC Human em_rel_htc_hum
ENA Sequence HTG Human em_rel_htg_hum
ENA Sequence Patent Human em_rel_pat_hum
ENA Sequence Standard Human em_rel_std_hum
ENA Sequence STS Human em_rel_sts_hum
ENA Sequence Invertebrate Sequences from invertebrate organisms. em_rel_inv
ENA Sequence EST Invertebrate em_rel_est_inv
ENA Sequence GSS Invertebrate em_rel_gss_inv
ENA Sequence HTC Invertebrate em_rel_htc_inv
ENA Sequence HTG Invertebrate em_rel_htg_inv
ENA Sequence Patent Invertebrate em_rel_pat_inv
ENA Sequence Standard Invertebrate em_rel_std_inv
ENA Sequence STS Invertebrate em_rel_sts_inv
ENA Sequence TSA Invertebrate em_rel_tsa_inv
ENA Sequence Mammal Sequences from mammals, excluding rodents and humans. em_rel_mam
ENA Sequence EST Mammal em_rel_est_mam
ENA Sequence GSS Mammal em_rel_gss_mam
ENA Sequence HTC Mammal em_rel_htc_mam
ENA Sequence HTG Mammal em_rel_htg_mam
ENA Sequence Patent Mammal em_rel_pat_mam
ENA Sequence Standard Mammal em_rel_std_mam
ENA Sequence STS Mammal em_rel_sts_mam
ENA Sequence TSA Mammal em_rel_tsa_mam
ENA Sequence Mouse Sequences from mus musculus. em_rel_mus
ENA Sequence EST Mouse em_rel_est_mus
ENA Sequence GSS Mouse em_rel_gss_mus
ENA Sequence HTC Mouse em_rel_htc_mus
ENA Sequence HTG Mouse em_rel_htg_mus
ENA Sequence Patent Mouse em_rel_pat_mus
ENA Sequence Standard Mouse em_rel_std_mus
ENA Sequence STS Mouse em_rel_sts_mus
ENA Sequence Phage Sequences from bacteria phages. em_rel_phg
ENA Sequence GSS Phage em_rel_gss_phg
ENA Sequence HTG Phage em_rel_htg_phg
ENA Sequence Patent Phage em_rel_pat_phg
ENA Sequence Standard Phage em_rel_std_phg
ENA Sequence Plant Sequences from plants. em_rel_pln
ENA Sequence EST Plant em_rel_est_pln
ENA Sequence GSS Plant em_rel_gss_pln
ENA Sequence HTC Plant em_rel_htc_pln
ENA Sequence HTG Plant em_rel_htg_pln
ENA Sequence Patent Plant em_rel_pat_pln
ENA Sequence Standard Plant em_rel_std_pln
ENA Sequence STS Plant em_rel_sts_pln
ENA Sequence TSA Plant em_rel_tsa_pln
ENA Sequence Prokaryote Sequences from prokaryotes. em_rel_pro
ENA Sequence EST Prokaryote em_rel_est_pro
ENA Sequence GSS Prokaryote em_rel_gss_pro
ENA Sequence HTC Prokaryote em_rel_htc_pro
ENA Sequence HTG Prokaryote em_rel_htg_pro
ENA Sequence Patent Prokaryote em_rel_pat_pro
ENA Sequence Standard Prokaryote em_rel_std_pro
ENA Sequence STS Prokaryote em_rel_sts_pro
ENA Sequence TSA Prokaryote em_rel_tsa_pro
ENA Sequence Rodent Sequences from rodents, but not mouse. em_rel_rod
ENA Sequence EST Rodent em_rel_est_rod
ENA Sequence GSS Rodent em_rel_gss_rod
ENA Sequence HTC Rodent em_rel_htc_rod
ENA Sequence HTG Rodent em_rel_htg_rod
ENA Sequence Patent Rodent em_rel_pat_rod
ENA Sequence Standard Rodent em_rel_std_rod
ENA Sequence STS Rodent em_rel_sts_rod
ENA Sequence TSA Rodent em_rel_tsa_rod
ENA Sequence Synthetic Sequences from synthetic constructs. em_rel_syn
ENA Sequence Patent Synthetic em_rel_pat_syn
ENA Sequence Standard Synthetic em_rel_std_syn
ENA Sequence Transgenic Sequences from transgenic constructs. em_rel_tgn
ENA Sequence Standard Transgenic em_rel_std_tgn
ENA Sequence GSS Transgenic em_rel_gss_tgn
ENA Sequence Unclassified Sequences from unspecified origin. em_rel_unc
ENA Sequence EST Unclassified em_rel_est_unc
ENA Sequence Patent Unclassified em_rel_pat_unc
ENA Sequence Standard Unclassified em_rel_std_unc
ENA Sequence Viral Sequences from Viruses. em_rel_vrl
ENA Sequence EST Viral em_rel_est_vrl
ENA Sequence GSS Viral em_rel_gss_vrl
ENA Sequence HTG Viral em_rel_htg_vrl
ENA Sequence Patent Viral em_rel_pat_vrl
ENA Sequence Standard Viral em_rel_std_vrl
ENA Sequence TSA Viral em_rel_tsa_vrl
ENA Sequence Vertebrate Sequences from vertebrates, excluding human, mouse and rodents. em_rel_vrt
ENA Sequence EST Vertebrate em_rel_est_vrt
ENA Sequence GSS Vertebrate em_rel_gss_vrt
ENA Sequence HTC Vertebrate em_rel_htc_vrt
ENA Sequence HTG Vertebrate em_rel_htg_vrt
ENA Sequence Patent Vertebrate em_rel_pat_vrt
ENA Sequence Standard Vertebrate em_rel_std_vrt
ENA Sequence STS Vertebrate em_rel_sts_vrt
ENA Sequence TSA Vertebrate em_rel_tsa_vrt
ENA Sequence Updates Daily updates to the quarterly ENA Sequence release emnew
EMBL Coding Sequence The nucleotide sequences of the coding sequence (CDS) features in the EMBL nucleotide sequence databank (EMBL-Bank). emblcds
Others
ENA Sequence Expressed Sequence Tag em_rel_est
ENA Sequence Genome Survey Sequence em_rel_gss
ENA Sequence High Throughput cDNA em_rel_htc
ENA Sequence High Throughput Genome em_rel_htg
ENA Sequence Patent em_rel_pat
ENA Sequence Standard em_rel_std
ENA Sequence Sequence Tagged Site em_rel_sts
ENA Sequence Transcriptome Shotgun Assembly em_rel_tsa
ENA Sequence Release and Updates emall
ENA Sequence Vectors Sequencing vectors extracted from the ENA Sequence emvec
IMGT
IMGT/LIGM-DB The immunoglobulins and T cell receptors (LIGM-DB) section of the international immunogenetics (IMGT) database imgtligm
IMGT/HLA The human major histocompatibility complex (HLA) section of the the international immunogenetics (IMGT) database imgthla
IPD-KIR Human Killer-cell Immunoglobulin-like Receptors (KIR) sequence in the Immuno Polymorphism Database (IPD) ipdkir
IPD-MHC Major Histocompatibility Complex (MHC) section of the Immuno Polymorphism Database (IPD) ipdmhc
Patents
NR Patent DNAs Level-1 Non-redundant Patent DNAs sequences Level 1 covering patent data from the ENA Sequence nrnl1
NR Patent DNAs Level-2 Non-redundant Patent DNAs sequences Level 2 covering patent data from the ENA Sequence nrnl2
Structure
Nucleotide Structure Sequences Nucleotide sequences from structures described in the Brookhaven Protein Data Bank(PDB) pdbna

Default value is: ENA Sequence TSA Vertebrate [em_rel_tsa_vrt]

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

Default value is: dust

View Filter

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

Default value is: yes [true]

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.

Default value is: both

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