Home About MiGAP

What is MiGAP?

The number of bacterial genomes collected by Genome Information Broker of DDBJ [2] has increased every week and will reach 1000 genomes in September 2009. Thanks to the revolution of the sequencing technology, many microbiologists will get genome sequences of their favorite strains. It is certain that we will soon observe tsunami of genome sequences. However, it is uncertain that every microbiologist is able to fully utilize the genome sequence for their research. The biological knowledge will remain only a drop in the ocean, if the bottleneck is not removed. The bottleneck is the annotation. Therefore, we have developed a microbial genome annotation pipeline (MiGAP) to support for novice and old pro alike to interpret sequences.


More than 1,000 microbial complete genomes have been sequenced as of December 2009 and the rate of sequencing will rocket ahead thanks to the 2nd and 3rd generation sequencers. However, the tsunami of sequence data does not necessarily mean the increase of our knowledge on microbes. The sequences have to be annotated. MiGAP (Microbial Genome Annotation Pipeline) provides novice and old pro alike with a mechanical annotation to microbial contigs and genomes.

MiGAP identifies ORFs and RNA regions and infers the functions of ORFs by referring to highly evaluated public databases. MiGAP has the following three modes of the operation:

b-MiGAP provides analysis by the default setting of programs, parameters and the reference databases. The user is required to just give sequences to MiGAP to get the annotation

s-MiGAP provides the user with the freedom to select programs, parameters and the reference databases.

g-MiGAP provides the user with the function of add his/her own tools and databases to the pipeline in addition to s-MiGAP function.

Please get UserID from DNA Data Bank of Japan, National Institute of Genetics to start using MiGAP. The URL of the user registration is https://www.ddbj.nig.ac.jp/cgi-bin/acc30-apl.cgi.

Good Luck.


MiGAP is in the public domain. However, it is requested that in any subsequent use of this work, MiGAP be given appropriate acknowledgment. Please refer to the list of publications.

The MiGAP team does not warrant or assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any functions and output.