Mini-tutorials for common use-cases and to address frequently asked questions FAQs
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.
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.
OmicsBox allows combining two Functional Anlaysis projects which contain either have the same identifiers or different ones.
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? 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
It is possible to perform a Fisher Exact Test on the 2 groups even if the annotation is in different files (.annot). First, both .annot files (group 1 and group 2) need to be loaded into Blast2GO.The test and reference set have to be generated according to the groups you want to compare. These are normal text files with the
This article explains what a Gene Set Enrichment Analysis (GSEA) is, how it works and how to use it with OmicsBox. What is an enrichment analysis? Enrichment analyses are a family of bioinformatics methods that aim to facilitate the biological interpretation of many bioinformatics results. Among these, the methods based on gene sets analysis are particularly helpful and widespread. The
OmicsBox/Blast2GO can handle big data, but it needs plenty of free disk space in the systems temporary files folder. If you run into troubles with a shortage of disk space, follow this guide to manually change the location of the folder for Blast2GO temporary files to e.g. another partition.
OmicsBox/Blast2GO automatically reserves up to 80% of the available system memory (i.e. RAM), which is fine in most cases. However, sometimes and especially on Linux, this can lead to excessive swapping and will slow down Blast2GO. Follow this guide to manually change the maximum amount of memory Blast2GO will be allowed to use.
