Blast2GO protocols

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Blast2GO specifications


Unique identifier OMICS_01475
Name Blast2GO
Alternative name Blast 2 GO
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 5.0
Stability Stable
Registration required Yes
Maintained Yes



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Publications for Blast2GO

Blast2GO in pipelines

PMCID: 5753516
PMID: 29298661
DOI: 10.1186/s12863-017-0592-5

[…] information resource (pir); protein data bank (pdb). unigenes annotatation and characteristics of homology search of unigenes against the nr database. similarly, we obtained go annotations by blast2go ( [, ]. kegg pathway annotation and kegg orthology assignments were obtained with the kegg automatic annotation server []., according to the results […]

PMCID: 5755334
PMID: 29301488
DOI: 10.1186/s12870-017-1217-x

[…] to measure the distance was a binary metric., to annotate the reference genes, the sequences of annotated genes were used as queries in the blastx searches against the swiss-prot database, using the blast2go with default parameters []. then, gene ontology (go) terms were assigned for annotated genes. enrichment analysis of go was conducted using the tool ontologizer with a background […]

PMCID: 5766104
PMID: 29329292
DOI: 10.1371/journal.pone.0189898

[…] protein coding genes were supported by consistently high e-values (42% of the blast hits had e-value >1e-100; see e-value distribution in )., our gene ontology (go) term assignment [] via blast2go [] revealed 78% of the putative genes had an interpro hit, and 46% had a go annotation (). longer sequences were more likely to be annotated than shorter ones (see ): approximately 50% […]

PMCID: 5766596
PMID: 29330436
DOI: 10.1038/s41598-017-18534-0

[…] (, kegg (, and swissprot ( we generated gene ontology (go) annotations for our unigenes with blast2go v2.5.0, and used interproscan5 v5.11–51.0 to generate interpro ( annotations., we selected the segment of each unigene that best mapped to one […]

PMCID: 5767605
PMID: 29375398
DOI: 10.3389/fphys.2017.01127

[…] using blast against the nr, swissprot, kegg, and kog databases, with a cut-off value of 1e-5, and the highest sequence similarity targets selected for functional annotation of the transcripts. next, blast2go was used to perform go annotation of the transcripts (conesa et al., ; götz et al., ). finally, the molecular function, biological process, and cellular component of the genes were assigned […]

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Blast2GO in publications

PMCID: 5952850
PMID: 29785177
DOI: 10.1186/s41065-018-0060-x

[…] no redundant (nr) protein database (ncbi), swiss prot database, kegg (kyoto encyclopedia of genes and genomes), cog (clusters of orthologous groups) and interpro database with an e-value<10− 5. blast2go software was used for gene ontology (go) annotation., the equivalent mixed rna samples (young leaves, stems and roots) from three individuals of c. finetiana which used for transcriptome […]

PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] taxa was reconstructed using iq-tree, based on 29 proteins (longer than 50 aa) encoded by single-copy genes. the go names and subcellular protein locations of the fiscogs were predicted using blast2go v5.0 and the multiloc2 webserver against the fungal high-resolution database, respectively (, )., all four harpellales taxa and corresponding genome information have been deposited […]

PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] uniref100-databases containing clustered sets of proteins from uniprot, pfam-database of protein families and kegg-database of metabolic pathways. go analysis of protein sequences were conducted by blast2go []. go enrichment was performed by cluego with p value < 0.05 []., to construct the phylogenomic tree of c. pseudoreteaudii and 13 other ascomycota isolates, including botrytis cinerea, […]

PMCID: 5941469
PMID: 29739322
DOI: 10.1186/s12870-018-1296-3

[…] minmatch, and minscore set to 0.95, 35, and 35, respectively, and all other parameters set to default. we used blast [] to align unigenes to nt, nr, cog, kegg and swissprot to obtain annotations, blast2go (version: v2.5.0; parameters: default) [] with nr annotation to obtain go annotations, and interproscan5 [] to obtain interpro annotations. clean reads were mapped to unigenes using bowtie2 […]

PMCID: 5940786
PMID: 29739966
DOI: 10.1038/s41598-018-23874-6

[…] and, respectively. additionally, a kyoto encyclopedia of genes and genomes (kegg) pathway enrichment analysis was conducted using blast2go., protein spots with average intensities that did not significantly deviate from the mid-parent values (p > 0.05) were considered to correspond to additively accumulated proteins. […]

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Blast2GO institution(s)
Bioinformatics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
Blast2GO funding source(s)
Supported by the Spanish Ramon y Cajal Program and the National Institute of Bioinformatics (a platform of Genoma Espana).

Blast2GO reviews

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Josh Faber-Hammond

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Overall this program is easy to use, but I have many complaints about how commercial it has become. The free version has become virtually unusable for even relatively small NGS dataset due to speed and lack of very basic functionality (such as selecting sequences by name).
Above all else though, consider this a warning to anyone who wants to use the basic version for their analysis. BLAST2GO BASIC WITHHOLDS YOUR RESULTS AND DOESN'T NOTIFY YOU. I ran enrichment analysis side by side with the PRO and Basic versions of the software with the exact same input dataset and parameters. Enrichment analysis with the basic version gave me no significantly enriched GO categories, while the PRO version gave me many expected enriched GO categories for my dataset. Had I not done the side-by-side analysis I easily could have tried to publish false results showing that there were no significantly enriched GO categories in my dataset, and I never would have known otherwise.
Other functions are grayed out in the basic version, showing that you need to pay to gain access to that tool, while they leave a nonfunctional version of the enrichment test in there. While I generally can get behind entrepreneurship, Blast2GO's push for people to buy their PRO package is dishonest and may have led to the publication of countless false results. Who knows what other Blast2GO Basic functions are secretly withholding results. If anyone else is so inclined, please do your own tests to find out and let others know.

Amr Galal

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Blast2Go is very very great tool makes very much work in less time than using many different tools