| |
Promoter analysis
- co-expressed genes clustering workflows:
Protocol description: clustering of genes based on
the pairwise alignment of their TFBSs maps. Such protocol can be used to validate the clustering of gene expression data.
To facilitate its execution, we have prepared a data submission page. You can either submit a list of ENSEMBL genes or a set of FASTA promoter sequences.
The protocol has also been implemented using taverna software. You can download the workflows and load them in your local taverna installation.
Taverna Input document examples:
These workflows have been successfully tested with taverna release v1.5.1.6.
ESTs assembly
input: chromatograms data
Output: the read sequences and associated quality data as well as the phrap assembly data
Protocol description
Picture of this implemented workflow (using Taverna): ESTs_Assembly_Workflow_taverna
Download the taverna workflow.
Gene predictions
All the following Workflows have been implemented using taverna software. You can download the workflows and load them in your local taverna installation.
- GeneID workflows:
The following workflow takes a genomic sequence in FASTA
format, runs geneid, then translates the gene
predictions into a set of peptide sequences in order to
run various software (blastp, pfam search etc.) that take peptide sequence input,
giving some hints about the function of the predicted genes.
Taverna Input document example:
- SGP2 workflows:
SGP2 software is an adaptation of geneid that takes into
account synteny data, in order to improve the accurracy of
the predictions.
The synteny data are computed using a syntenic sequence
from another organism and by performing tblastx search.
The following workflow takes two syntenic sequences in FASTA
format, runs tblastx, then runs SGP2 on the sequence you
wish to perform the gene predictions, and finally translates the gene
predictions into a set of peptide sequences.
Taverna Input document example:
- Workflows running both geneid and SGP2:
The following workflow runs both geneid and SGP2 and
generates an annotation map using gff2ps to visualize the
annotations in order to compare them.
Taverna Input document example:
The following workflow is very similar to the previous one. In
addition, it also takes a reference set of gene
annotations in GFF format that can be compared to the predictions from
geneid and SGP2.
Taverna Input document example:
|
