The Coloured Graph option is a function in Blast2GO which allows to combine and visualize multiple functional profiles within one GO graph. For each group or profile a different color can be assigned and the resulting GO graph can be filtered and colored accordingly. This video shows how to create a text files to generate a Coloured Graph for three
This tutorial shows how to use the Generic Table and the “Select” functions in Blast2GO to identify sequences based on its biological functions and how to create and combine ID lists. These lists can be saved and used in downstream analysis like e.g. enrichment analysis. In Blast2GO, sequences are shown in table format. Per default, annotation projects use the Blast2GO
OmicsBox allows performing functional enrichment analysis with a Fisher’s Exact Test. It is a statistical test based on contingency tables to study the significance of the association between two kind of classifications. OmicsBox allows to apply this test to Gene Ontology functional annotations and other labels and to compare different gene lists against each other. This is used to identify
This short video shows how to use BioMart and GO-Slim to download and review the whole human genome functional annotation with Blast2GO. BioMart allows you to download the functional annotations of many different organisms directly into Blast2GO. BioMart offers many different identifiers like e.g. UniProt, Ensembl, HGNC, etc. Additionally to the annotations, it is also possible to obtain the protein
Blast2GO allows you to create your own Blast database from a single or multi-species FASTA file using the option “Make Blast Database“. Once the database is formatted it can be used to run a local Blast.
Blast2GO allows search for non-coding RNA (ncRNA) families and other structured RNA elements sequences via the RFAM webservice. The RFAM database is a collection of RNA families, categorized into three functional classes: non-coding RNA genes structured cis-regulatory elements self-splicing RNAs The RFAM algorithm allows via alignments to search this database and classify your sequence dataset. This might be interesting for contigs obtained via
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.
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.
How to know if all your sequences have been analyzed The Analysis Progress chart is a very useful representation, which shows the step of the analysis in which the sequences in your dataset are found. They can be in different states, each represented by a color: Total: grey Without Analysis: white With IPS: purple With Blast Hits: orange Without Blast
