In silico mining in expressed sequences of Neurospora crassa for identification and abundance of microsatellites.
In the present study, 3217 UniGene sequences of Neurospora crassa downloaded from the National Center for Biotechnology Information (NCBI) were mined for the identification of microsatellites or simple sequence repeats (SSRs). A total of 287 SSRs detected gives density of 1SSR/14.6 kb of 4187.86 kb sequences mined suggests that only 250 (7.8%) of sequences contained SSRs. Depending on the repeat units, the length of SSRs ranged from 14 to 17 bp for mono-, 14 to 48 bp for di-, 18 to 90 bp for tri-, 24 to 48 bp for tetra-, 30 for penta- and 42 to 48 bp for hexa-nucleotide repeats. Tri-nucleotide repeats were the most frequent repeat type (88.8%) followed by di-nucleotide repeats (5.9%). An attempt was also made with the help of bioinformatics approach to find out primer pairs for identified SSRs and primers were found only for 239 sequences. But, this part needs experimental validation. Annotation of SSRs containing sequences was also carried out.
Shanker
Asheesh
A
Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali-304022, Rajasthan, India. ashomics@rediffmail.com
Singh
Ashutosh
A
Sharma
Vinay
V
D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D018895:Microsatellite Repeats / Q000235:genetics*; D009492:Neurospora crassa / Q000235:genetics*; D013045:Species Specificity; D014158:Transcription, Genetic