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Basic Transcriptome Characterization with Blast2GO

Analysis workflow Objective: To describe the process of a transcriptome characterization using Blast2GO. Input data: A mouse RNA-seq dataset composed of 140803 contigs. Pipeline: Blastx and InterproScan were performed with the complete dataset to identify proteins. Sequences with no Blastx hits nor IPS results were selected and further analyzed. RFAM and Local Blast (against an EST mouse db) were performed with the sequences with

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Retrieve Top Blast Hit

How to change sequence names coming from Prokaryotic GeneFinding

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

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Generate Venn Diagram

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

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new version 5

New RNA-Seq Features in Blast2GO 5

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.

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Load Tair Gene Ids from Biomart

Load Sequences/ Annotation from a list of identifiers within Blast2GO

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.

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Load exon sequences from reference

Load FASTA sequences from Reference and GFF file

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.

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