Local Sequence Similarity Search

Objective: Perform sequence similarity search against sequences stored in the hard drive of your personal computer.

Sequence similarity search is usually done through public domains such as NCBI or through your organization’s facility. NCBI provides a free-access service and does a great job. However, since the workload for NCBI is huge, it may take a long period of time to retrieve data. There are many cases in which you only want a quick similarity search against a limited data set such as the curated human mRNA database. The Local Sequence Similarity Search in GeneLooper™ 2.0 can just do that in your personal computer and has some unique features. It is extremely useful to search one member of a gene family against all other members of the family saved in a common folder, or search similarities among the members of a cluster saved in a folder created by the Sequence Clustering utility (see Sequence Clustering for detail).

Features:

1. Easy to set up and flexible database files: use “.seq” files, Q-fasta files or a mixture of the two as long as the files are in a common folder.
2. Provide a whole sequence alignment instead of fragmented alignments for every positive sequence.
3. Provide open reading frame information.
4. Adjustable search stringency.
5. Reliable: uses your own computer so you can count on it.