Blast2GO Blog

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How to change sequence name 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.

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Generate a Venn Diagram in Blast2GO

When running a pairwise differential expression analysis, I was interested in rapidly visualise the genes that overlap between KOvsCtrl, TretvsCtrl and KOvsTret comparisons.

The Venn Diagram tool offered by Blast2GO allows to select multiple ID lists or ID value list in text or B2G format and draw the intersection of the elements of the lists.

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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.


Load Sequences/ Annotation from a list of identifiers within Blast2GO

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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How to load Fasta sequences from a whole genome using a GFF/GTF?

Sometimes databases provide the whole genome and the GFF or GTF files but not the exon or CDS FASTA files.
With Blast2GO it is possible to extract the exons or the CDS from the genome using the GFF file.

 

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How to rename the sequence name?

Blast2GO allows renaming the name of all selected sequences by converting, replacing or adding text to the actual sequence name.

 

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How to combine two projects in Blast2GO?

Blast2GO allows combining two projects which contain either the same identifiers or different ones.

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Blast2GO Poster at the ECCB 2018

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.

 

Functional Genomics Analysis of Newly Sequenced Genomes From Scratch with Blast2GO

Functional genomics attempts to describe functions of genes and proteins by making use of data derived from genomic and transcriptomic experiments. The combination of omics data allows to better understand the relationship between genotype and phenotype on a system-wide scale.


Download poster.

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NGS data preprocessing and quality control: How-To with Blast2GO

Functional genomics attempts to describe functions of genes and proteins by making use of data derived from genomic and transcriptomic experiments. Some bioinformatics tools, like Blast2GO, offers biologists to get from raw NGS data through all steps up to the generation of biological insights for a species without any previous genome resources. 

The bioinformatic process to perform a de novo transcriptomic analysis can be divided into 4 phases: 

  1. Quality check and pre-processing raw sequence data
  2. De novo transcript reconstruction and functional characterization
  3. Expression quantification and differential expression analysis
  4. Functional Enrichment Analysis 

In this article, we will analyze the first point and we will explain how to perform NGS data preprocessing and quality control of raw sequence data. 

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Blast2GO Supported Project:

Gene expression profiling of colonial green alga Volvox carteri

Researchers:

  • Mrs. Soulmaz Ekhtari
  • Teachers: Dr. Jafar Razeghi, Dr. Karim Hasanpur, and Dr. Arash Kianianmomeni

Volvox carteri is a species of colonial green algae that forms large spherical colonies (up to 1.5 mm)(Image: Wikipedia)

Background and Project Overview:

The evolutionary origin of some multicellular organisms has not yet been completely studied. A clear characteristic of complex multicellular organisms is germ-soma differentiation.
The monophyletic group of volvocine contains multiple algae species ranging from unicellular species such as Chlamydomonas reinhardtii to the multicellular genus Volvox. The fresh-water, clonal green alga, Volvox carteri composed of about 2000–4000 small, motile somatic cells, which construct a monolayer at the surface of a spheroid, and around 16 much larger, immotile reproductive cells within the surface. The organization of V. carteri is very simple and regular. In the volvocine algae (Volvocales), only V. carteri possess a primary division of labour. The V. carteri provides a good opportunity to investigate the molecular mechanisms of evolutionary transition from unicellularity to multicellularity in the eukaryotic world.
In this study, the RNA-seq approach was employed to investigate the transcriptome profiling of two separated cell types of V.carteri.

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