Online Software Tools




Our computation resources, including a 138 processor UNIX cluster, allows us to offer certain software tools free to users. Currently, we have four tools relating to sequence analysis, but we plan to add to this list in the near future.

BLAST

Compare your sequences to numerous public sequence databases. (Altshcul et al., 1990)

FASTA

Compare your sequences to numerous public sequence databases. (Pearson & Lipman, 1998)

SSR Miner

Look for microsatellites and primers in your sequences. (Microsatellite mining approach loosely based on Temnykh et al., 2001; Primer3 citation is Rozen & Skaletsky, 2000)

CAP3

Assemble your sequences at varying stringencies. (Huang & Madan, 1999)


References for Software

If you obtain results through our online interface, please cite the original author of the software when publishing. The link will take you to NCBI's Pubmed reference with further information.


Altschul SF, Gish W, Miller W, Myers EW, and Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215(3):403-410.


Huang X and Madan A. 1999. CAP3: A DNA sequence assembly program. Genome Res. 9(9):868-877.


Pearson WR and Lipman DJ. 1988. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85:2444-2448.


Rozen S and Skaletsky H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 132:365-86.


Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S and McCouch S. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11:1441-1452.