How to create a gene list within OmicsBox/Blast2GO to run the functional enrichment analysis
Mariana Monteiro November 13, 2018
This article explains how to create ID lists of either Blast results or differential expressed genes in Blast2GO.
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How to change sequence names coming from Prokaryotic GeneFinding
Mariana Monteiro November 12, 2018
When running GeneFinding the sequences receive a name with the predicted genes. The first part of the sequence identifier comes from the genome reference sequence name (de-novo assembly) and then a _orfx is appended, where x is a number. Sometimes this name is not useful to proceed with downstream analysis or compare results from other experiments. Is there any way
Generate Venn Diagram
Mariana Monteiro November 6, 2018
A Venn Diagram is a graphical representation of sets or groups of elements or IDs in form of circles where common elements/IDs of the sets are represented by the areas of overlap among the circles. In bioinformatics this is a popular graphical representation to compare subsets, for example when running a pairwise differential expression analysis it might be interesting to
Load Sequences/ Annotation from a list of identifiers within Blast2GO
Mariana Monteiro October 30, 2018
OmicsBox/Blast2GO offers two different features to retrieve the gene/protein sequences as well as the corresponding annotation from a list of identifiers within Blast2GO PRO. Both features can be found under File > Load > Load Annotations. The expected input file is a text file with the identifiers in a single column without a header.
Load FASTA sequences from Reference and GFF file
Mariana Monteiro October 26, 2018
Sometimes databases provide the whole genome and the GFF or GTF files but not the exon or CDS FASTA files.With OmicsBox/Blast2GO it is possible to load a Fasta sequences and to extract the exons or the CDS from the genome using the GFF file.
How to rename the sequence name in OmicsBox
Mariana Monteiro October 25, 2018
OmicsBox allows renaming the name of all selected sequences by converting, replacing or adding text to the actual sequence name.
How to combine two projects in OmicsBox
Mariana Monteiro October 23, 2018
OmicsBox allows combining two Functional Anlaysis projects which contain either have the same identifiers or different ones.
CloudBlast and CloudIPS finished, but there are still white sequences.
Mariana Monteiro March 16, 2017
CloudBlast and CloudIPS need Cloud Units to work.If all Cloud Units have been consumed CloudBlast and CloudIPS will stop. Consumption depends on what you are doing. The most costly (in terms of computation time) analysis is definitely to do a blastx against the whole NR with very long sequences. The smaller the database used the less Cloud Units are used. Use the taxonomy
After loading the sequences, the run blast icon is greyed out in OmicsBox, why?
Mariana Monteiro February 25, 2017
It is possible to load more than one project into OmicsBox and each project will be displayed in a different tab. So to run the analysis on the different projects you will need to have the OmicsBox table active (white tab). In your case, probably the Progress tab or the Messages tab is active and therefore you cannot analyse your