FusariumSSRDB

FuasriumSSRDB provides information about microsatellites of both kinds, i.e. perfect (mono- to hexa-nucleotide) and compound along with their size, starting and ending bp in all the genes of each Fusarium species.  For each of the SSR identified, primers are also provided along with the related information.

Complete genome sequence

Complete genome sequence for each of these Fusarium species was obtained from Broad Institute of Harvard and MIT, which had completed sequencing and annotation for these members of Fusarium group. Any further information regarding sequence, function, annotation or gene of these Fusarium sps. can be obtained from Broad Institute of Harvard and MIT.

SSR Identification Process

Both perfect and compound SSRs were identified in these species. SSRs were identified using MISA (Microsatellite Indentification tool) available at http://pgrc.ipk-gatersleben.de/misa/misa.html. Following criteria was used for motifs search:

i. At least 10 bp length (i.e., mono-nucleotide >=10; di-nucleotide >=6; tri-nucleotide >=5; tetra- nucleotide >=5; penta-nucleotide >=5 and hexa-nucleotide >=5) and

ii. Minimum difference between two SSRs in a sequence (interruption) was 100 bases.

Primer Designing for identified SSRs

For all the SSRs identified in these Fusarium sps., attempts were taken to design primer pairs through Primer3 which is available at http://primer3.sourceforge.net/.

Conditions used for primer designing were:

i. 50– 61°C melting temperature,

ii. 18– 24 bp primer length and

iii. product size range 100-280.