Coffee SSR: Difference between revisions
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m New page: ==Summary== A total of 13175 C. canephora unigenes were downloaded from the internet database( ftp://ftp.sgn.cornell.edu/coffee/). The sequences were screened for the presence of di, tri t... |
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==Summary== | ==Summary== | ||
<pre> | |||
A total of 13175 C. canephora unigenes were downloaded from the internet | A total of 13175 C. canephora unigenes were downloaded from the internet | ||
database( ftp://ftp.sgn.cornell.edu/coffee/). The sequences were | database( ftp://ftp.sgn.cornell.edu/coffee/). The sequences were | ||
screened for the presence of di, tri tetra, penta and hexa nucleotide | screened for the presence of di, tri tetra, penta and hexa nucleotide | ||
repeat motifs using MISA perl scripts | repeat motifs using MISA perl scripts | ||
(http://pgrc.ipk-gatersleben.de/misa/download/misa.pl). The parameters | (http://pgrc.ipk-gatersleben.de/misa/download/misa.pl). | ||
are configured to have minimum threshold of 2-8 3-6 4-5 5-5 6-5 (di | |||
repeats 8 times). The SSR co-ordinates were marked on the unigenes and | The parameters are configured to have minimum threshold of 2-8 3-6 4-5 5-5 6-5 | ||
(di repeats 8 times). The SSR co-ordinates were marked on the unigenes and | |||
primers were designed on the flanking region so as to have PCR product | primers were designed on the flanking region so as to have PCR product | ||
length of ___ to ___ using Primer3 | length of ___ to ___ using Primer3 | ||
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further filtered used desired primer model. The results obtained are | further filtered used desired primer model. The results obtained are | ||
summarised in the Table below | summarised in the Table below | ||
</pre> | |||
Revision as of 01:06, 23 August 2008
Summary
A total of 13175 C. canephora unigenes were downloaded from the internet database( ftp://ftp.sgn.cornell.edu/coffee/). The sequences were screened for the presence of di, tri tetra, penta and hexa nucleotide repeat motifs using MISA perl scripts (http://pgrc.ipk-gatersleben.de/misa/download/misa.pl). The parameters are configured to have minimum threshold of 2-8 3-6 4-5 5-5 6-5 (di repeats 8 times). The SSR co-ordinates were marked on the unigenes and primers were designed on the flanking region so as to have PCR product length of ___ to ___ using Primer3 (http://sourceforge.net/projects/primer3) perl scripts with default parameters. The complete perl pipeline involves series of steps viz., idenfying the repeats, marking the repeat co-ordinates, parsing the results, converting the results into Primer3 input format, Running Primer3, parsing and converting the Primer3 output in GFF format. The entire pipeline was automated using perl, while each step was considered as a module. Of the 13175 sequences examined 510 SSR's were identified in 476 sequences. 31 sequences conrtained more than 1 SSR. The primers were further filtered used desired primer model. The results obtained are summarised in the Table below