This article explains how to start functional enrichment analysis of pairwise differential genes in Blast2GO.
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
This article explains how to create ID lists of either Blast results or differential expressed genes in Blast2GO.
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
This video shows an overview of new RNA-Seq features in Blast2GO 5: FastQ Quality Control and Preprocessing, de novo Transcriptome Assembly, Transcript Quantification and Differential Expression Analysis.
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.
BioBam Bioinformatics attended the 17th European Conference on Computational Biology ECCB in Athens, Greece. It is the main computational biology event in Europe and congregates scientists working in a variety of disciplines, including bioinformatics, computational biology, biotechnology, medicine, and systems biology. We presented all the new features developed, during the last month, in Blast2GO:
