Multi-Sequence Similarity Search

Objective: Perform high-throughput sequence similarity search against a sequence database and provide both a tabulated summary of similarity data and detailed whole sequence alignments of homologous sequences in document files.

Many public domains and private sectors provide free-access, web-based sequence blasting services using the Blast program (Basic local alignment tools). It has been proven to be very effective in searching sequence homology, especially against a large data set. However, most of these service sites only allow single sequence blast and provide a standard alignment report. To set up a high-throughput blast facility requires a great deal of equipment and human resource, furthermore, to tabulate the results of multiple sequence blasting data to a summary is quite challenging. Clearly, there is a demand for a search algorithm which is more flexible in selecting data sets, high-throughput, low-cost and with a better data presentation.

The Multi-Sequence Similarity Search utility in GeneLooper™ 2.0 is designed to accommodate this need. Since the program is Windows based and operates on a personal computer, it is only suitable for a relatively small data set and not for long genomic sequences. However it is very effective when performing multiple sequence similarity searches against a relatively small data set such as the whole transcripts of all human genes.

Features:

1. Search sequences in flexible data sets with adjustable searching parameters.
2. High-throughput: perform thousands of sequence similarity searches at once.
3. Instant data report: tabulate similarity data along with other pieces of useful information including accessions, lengths, ORF and proximal homologous locations of the two sequences.
4. Completed sequence alignments instead of fragmented alignments.
5. Saved sequences of queried and returned sequences in a common folder for further study.
6. A search process can be interrupted and resumed easily.