GeneWise

Introduction

The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.

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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 - Input Sequences

First Input Sequence

The protein 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.

First Sequence File Upload

A file containing a valid protein sequence in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot) can be used as input for the sequence comparison. Word processors files may yield unpredictable results as hidden/control characters may be present in the files. 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.

Second Input Sequence

The DNA sequence to be compared can be entered directly into the form. The sequence must be in a recognised format eg. GCG, FASTA, EMBL, GenBank. Partially formatted sequences are 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.

Second Sequence File Upload

A file containing valid a DNA sequence in any format (GCG, FASTA, EMBL, GenBank) can be used as input for the comparison. Word processor files may yield unpredictable results as hidden/control characters may be present in the files. 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.

Step 2 - Set alignment options

Show Parameters

Show parameters in the output alignmment, as in genewise.

Default value is: ON [true]

Pretty ASCII

Show pretty ASCII alignment viewing, as in genewise.

Default value is: ON [true]

Gene Structure

Show gene structure, as in genewise

Default value is: ON [true]

Protein Translation

Show protein translation, breaking at frameshifts.

Default value is: ON [true]

cDNA

Show cDNA, as in genewise.

Default value is: ON [true]

EMBL Feature Table

EMBL feature table format with CDS key.

Default value is: ON [true]

Ace File Gene Structure

Show Ace file gene structure, as in genewise.

Default value is: ON [true]

GFF Output

Show Gene Feature Format file, as in genewise.

Default value is: ON [true]

EMBL Feature For diana

Show EMBL FT format suitable for diana.

Default value is: ON [true]

Local/Global Mode

Model in local/global mode. You should only put the model in global mode if you expect your protein homolog to have homology from start to end to the gene in the DNA sequence.

Label Description Abbreviation
Local local
Global global

Default value is: Local [local]

Splice Site

Using splice model or GT/AG? Use the full blown model for splice sites, or a simplistic GT/AG. Generally if you are using a DNA sequence which is from human or worm, then leave this on. If you are using a very different (eg plant) species, switch it off.

Label Description Abbreviation
Modelled model
GT/AG only flat

Default value is: GT/AG only [flat]

Random (Null) Model

The probability of the model has to compared to an alternative model (in fact to all alternative models which are possible) to allow proper Bayesian inference. This causes considerable difficulty in these algorithms because from a algorithmical point of view we would probably like to use an alternative model which is a single state, like the random model in profile-HMMs, where we can simply 'log-odd' the scored model, whereas from a biological point of view we probably want to use a full gene predicting alternative model. In addition we need to account for the fact that the protein HMM or protein homolog probably does not extend over all the gene sequence, nor in fact does the gene have to be the only gene in the DNA sequence. This means that there are very good splice sites/poly-pyrimidine tracts outside of the 'matched' alignment can severely de-rail the alignment.

Label Description Abbreviation
Synchronous model syn
Flat model flat

Default value is: Synchronous model [syn]

Algorithm

The solutions is different in the genewise21:93 compared to the genewise 6:23 algorithms. (1) In 6:23 we force the external match portions of the homology model to be identical to the alternative model, thus cancelling each other out. This is a pretty gross approximation and is sort of equivalent to the intron tie'ing. It makes things algorithmically easier... However this means a) 6:23 is nowhere near a probabilistic model and b) you really have to used a tied intron model in 6:23 otherwise very bad edge effects (final introns being ridiculously long) occur. (2) In 21:93 we have a full probabilistic model on each side of the homology segment. This is not reported in the -pretty output but you can see it in the -alb output if you like. Do not trust the gene model outside of the homology segment however. By having these external gene model parts we can use all the gene model features safe in the knowledge that if the homology segments do not justify the match then the external part of the model will soak up the additional intron/py-tract/splice site biases.

Label Description Abbreviation
GeneWise 623 623
GeneWise 2193 2193

Default value is: GeneWise 623 [623]

Step 3 - 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

Using GeneWise in the Drosophila annotation experiment.
(2000 Apr) Genome research 10 (4) :547-8
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