Mass Blaster V1.0 – A Perl Gui Tool for Mass Sequence Blast and Gene Prediction

Abstract

There is a continuous need for similarity search and predictive tools for the isolation of protein function, coding region, non-coding region, genes, orthologs group and phylogenetic relation in modern biological research. Especially, similarity search tool like BLAST Altschul et al. (1990) and gene prediction tool GENEMARK HMM Lukashin and Borodovsky (1997) are very effective and trust worthy computational tools for locating domains and gene prediction respectively. Using such numerous tools in the discovery environment for routine analysis is often laborious and time-consuming. For example to perform a homology search for 200 different proteins for function identification, one has to submit the individual sequence to the BLAST service and then obtains the result. Some of the problems faced during this process are (1) Should do manually because most of the services do not have mass sequence submission for the BLAST search, even though NCBI BLAST has the multiple sequence submission facility, it has processing time limit restriction, also user has to wait for the individual sequence result until BLAST search is done for all the submitted sequences, (2) Error-prone – possibility of human error on doing repetitive task, (3) Time consuming – consume lots of time when done manually. So, MASS BLASTER (Figure 1) is developed keeping in mind that the process should be automated, to reduce time and error, and to produce the same result of what the service provider, without sacrificing the quality of the result.