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 |
|---|---|---|
| EMBL-Bank | 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. | |
| EMBL Release | The quarterly release of the EMBL nucleotide sequence databank (EMBL-Bank) | em_rel |
| EMBL Environmental | Sequences from Environmental Samples. | em_rel_env |
| EMBL EST Environmental | em_rel_est_env | |
| EMBL GSS Environmental | em_rel_gss_env | |
| EMBL HTC Environmental | em_rel_htc_env | |
| EMBL HTG Environmental | em_rel_htg_env | |
| EMBL Patent Environmental | em_rel_pat_env | |
| EMBL Standard Environmental | em_rel_std_env | |
| EMBL TSA Environmental | em_rel_tsa_env | |
| EMBL Fungi | Sequences from Fungi. | em_rel_fun |
| EMBL EST Fungi | em_rel_est_fun | |
| EMBL GSS Fungi | em_rel_gss_fun | |
| EMBL HTC Fungi | em_rel_htc_fun | |
| EMBL HTG Fungi | em_rel_htg_fun | |
| EMBL Patent Fungi | em_rel_pat_fun | |
| EMBL Standard Fungi | em_rel_std_fun | |
| EMBL STS Fungi | em_rel_sts_fun | |
| EMBL TSA Fungi | em_rel_tsa_fun | |
| EMBL Human | Sequences from Human. | em_rel_hum |
| EMBL EST Human | em_rel_est_hum | |
| EMBL GSS Human | em_rel_gss_hum | |
| EMBL HTC Human | em_rel_htc_hum | |
| EMBL HTG Human | em_rel_htg_hum | |
| EMBL Patent Human | em_rel_pat_hum | |
| EMBL Standard Human | em_rel_std_hum | |
| EMBL STS Human | em_rel_sts_hum | |
| EMBL Invertebrate | Sequences from invertebrate organisms. | em_rel_inv |
| EMBL EST Invertebrate | em_rel_est_inv | |
| EMBL GSS Invertebrate | em_rel_gss_inv | |
| EMBL HTC Invertebrate | em_rel_htc_inv | |
| EMBL HTG Invertebrate | em_rel_htg_inv | |
| EMBL Patent Invertebrate | em_rel_pat_inv | |
| EMBL Standard Invertebrate | em_rel_std_inv | |
| EMBL STS Invertebrate | em_rel_sts_inv | |
| EMBL TSA Invertebrate | em_rel_tsa_inv | |
| EMBL Mammal | Sequences from mammals, excluding rodents and humans. | em_rel_mam |
| EMBL EST Mammal | em_rel_est_mam | |
| EMBL GSS Mammal | em_rel_gss_mam | |
| EMBL HTC Mammal | em_rel_htc_mam | |
| EMBL HTG Mammal | em_rel_htg_mam | |
| EMBL Patent Mammal | em_rel_pat_mam | |
| EMBL Standard Mammal | em_rel_std_mam | |
| EMBL STS Mammal | em_rel_sts_mam | |
| EMBL TSA Mammal | em_rel_tsa_mam | |
| EMBL Mouse | Sequences from mus musculus. | em_rel_mus |
| EMBL EST Mouse | em_rel_est_mus | |
| EMBL GSS Mouse | em_rel_gss_mus | |
| EMBL HTC Mouse | em_rel_htc_mus | |
| EMBL HTG Mouse | em_rel_htg_mus | |
| EMBL Patent Mouse | em_rel_pat_mus | |
| EMBL Standard Mouse | em_rel_std_mus | |
| EMBL STS Mouse | em_rel_sts_mus | |
| EMBL Phage | Sequences from bacteria phages. | em_rel_phg |
| EMBL GSS Phage | em_rel_gss_phg | |
| EMBL HTG Phage | em_rel_htg_phg | |
| EMBL Patent Phage | em_rel_pat_phg | |
| EMBL Standard Phage | em_rel_std_phg | |
| EMBL Plant | Sequences from plants. | em_rel_pln |
| EMBL EST Plant | em_rel_est_pln | |
| EMBL GSS Plant | em_rel_gss_pln | |
| EMBL HTC Plant | em_rel_htc_pln | |
| EMBL HTG Plant | em_rel_htg_pln | |
| EMBL Patent Plant | em_rel_pat_pln | |
| EMBL Standard Plant | em_rel_std_pln | |
| EMBL STS Plant | em_rel_sts_pln | |
| EMBL TSA Plant | em_rel_tsa_pln | |
| EMBL Prokaryote | Sequences from prokaryotes. | em_rel_pro |
| EMBL EST Prokaryote | em_rel_est_pro | |
| EMBL GSS Prokaryote | em_rel_gss_pro | |
| EMBL HTC Prokaryote | em_rel_htc_pro | |
| EMBL HTG Prokaryote | em_rel_htg_pro | |
| EMBL Patent Prokaryote | em_rel_pat_pro | |
| EMBL Standard Prokaryote | em_rel_std_pro | |
| EMBL STS Prokaryote | em_rel_sts_pro | |
| EMBL TSA Prokaryote | em_rel_tsa_pro | |
| EMBL Rodent | Sequences from rodents, but not mouse. | em_rel_rod |
| EMBL EST Rodent | em_rel_est_rod | |
| EMBL GSS Rodent | em_rel_gss_rod | |
| EMBL HTC Rodent | em_rel_htc_rod | |
| EMBL HTG Rodent | em_rel_htg_rod | |
| EMBL Patent Rodent | em_rel_pat_rod | |
| EMBL Standard Rodent | em_rel_std_rod | |
| EMBL STS Rodent | em_rel_sts_rod | |
| EMBL TSA Rodent | em_rel_tsa_rod | |
| EMBL Synthetic | Sequences from synthetic constructs. | em_rel_syn |
| EMBL Patent Synthetic | em_rel_pat_syn | |
| EMBL Standard Synthetic | em_rel_std_syn | |
| EMBL Transgenic | Sequences from transgenic constructs. | em_rel_tgn |
| EMBL Standard Transgenic | em_rel_std_tgn | |
| EMBL GSS Transgenic | em_rel_gss_tgn | |
| EMBL Unclassified | Sequences from unspecified origin. | em_rel_unc |
| EMBL EST Unclassified | em_rel_est_unc | |
| EMBL Patent Unclassified | em_rel_pat_unc | |
| EMBL Standard Unclassified | em_rel_std_unc | |
| EMBL Viral | Sequences from Viruses. | em_rel_vrl |
| EMBL EST Viral | em_rel_est_vrl | |
| EMBL GSS Viral | em_rel_gss_vrl | |
| EMBL HTG Viral | em_rel_htg_vrl | |
| EMBL Patent Viral | em_rel_pat_vrl | |
| EMBL Standard Viral | em_rel_std_vrl | |
| EMBL TSA Viral | em_rel_tsa_vrl | |
| EMBL Vertebrate | Sequences from vertebrates, excluding human, mouse and rodents. | em_rel_vrt |
| EMBL EST Vertebrate | em_rel_est_vrt | |
| EMBL GSS Vertebrate | em_rel_gss_vrt | |
| EMBL HTC Vertebrate | em_rel_htc_vrt | |
| EMBL HTG Vertebrate | em_rel_htg_vrt | |
| EMBL Patent Vertebrate | em_rel_pat_vrt | |
| EMBL Standard Vertebrate | em_rel_std_vrt | |
| EMBL STS Vertebrate | em_rel_sts_vrt | |
| EMBL TSA Vertebrate | em_rel_tsa_vrt | |
| EMBL Updates | Daily updates to the quarterly EMBL nucleotide sequence databank (EMBL-Bank) release | emnew |
| EMBL Coding Sequence | The nucleotide sequences of the coding sequence (CDS) features in the EMBL nucleotide sequence databank (EMBL-Bank). | emblcds |
| Others | ||
| EMBL Expressed Sequence Tag | em_rel_est | |
| EMBL Genome Survey Sequence | em_rel_gss | |
| EMBL High Throughput cDNA | em_rel_htc | |
| EMBL High Throughput Genome | em_rel_htg | |
| EMBL Patent | em_rel_pat | |
| EMBL Standard | em_rel_std | |
| EMBL Sequence Tagged Site | em_rel_sts | |
| EMBL Transcriptome Shotgun Assembly | em_rel_tsa | |
| EMBL Release and Updates | emall | |
| EMBL Vectors | Sequencing vectors extracted from the EMBL nucleotide sequence databank (EMBL-Bank) | 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 EMBL-Bank | nrnl1 |
| NR Patent DNAs Level-2 | Non-redundant Patent DNAs sequences Level 2 covering patent data from the EMBL-Bank | nrnl2 |
| Structure | ||
| Nucleotide Structure Sequences | Nucleotide sequences from structures described in the Brookhaven Protein Data Bank(PDB) | pdbna |
Default value is: EMBL 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).