How to export Gene Finder GFF output with GO terms.
Mariana Monteiro
November 22, 2018
This article explains how to export a GFF file with GO terms in Blast2GO.
How to launch an Enrichment Analysis from pairwise differential expression results in OmicsBox
Mariana Monteiro
November 13, 2018
This article explains how to start functional enrichment analysis of pairwise differential genes in Blast2GO.
How to improve functional annotations using “Retrieve Blast Top-hit”
Jesus Gutierrez
November 13, 2018
RNA-seq data is sometimes difficult to match with proteins, due to the short length of the reads. When this is the case, it might be useful to try to find EST hits, which can then be used to find new protein matches. In this demo, we will show how to retrieve top EST hits and the different options that this tool
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.
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.
