Coffee SSR - Revision history

Raj: /* Summary */

2008-08-23T01:23:50Z

Summary

← Older revision		Revision as of 01:23, 23 August 2008
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	summarised in the Table below		summarised in the Table below
	</pre>		</pre>

			==Analysis==
			* The Coffee EST data can be accessed [http://www.mustard.rajkumar.in/data/coffee/ here]
			* The results can be accessed [http://www.mustard.rajkumar.in/user/jeena/misa/ here]



	[[Category:Projects]]		[[Category:Projects]]
	[[Category:~~Tobacco~~]]		[[Category:Bioinformatics]]
			[[Category:Coffee SSR]]

Raj at 01:20, 23 August 2008

2008-08-23T01:20:36Z

← Older revision		Revision as of 01:20, 23 August 2008
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	summarised in the Table below		summarised in the Table below
	</pre>		</pre>



			[[Category:Projects]]
			[[Category:Tobacco]]

Raj: /* Summary */

2008-08-23T01:06:28Z

Summary

← Older revision		Revision as of 01:06, 23 August 2008
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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
Line 21:		Line 23:
	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>

Raj: 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...

2008-08-23T01:02:55Z

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...

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 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