User:Jose Fabricio Lopez/Notebook/GEDF/2012/08/17: Difference between revisions

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===Trichoderma & A. thaliana interaction===
===Trichoderma & A. thaliana interaction===
==Trichoderma & A. thaliana interaction==
====Things to do====
====Things to do====
*Check plants
*Uncap the plants
====Things done====
*Check plants
===Loogbook===
*When I went to see the plants, some of them were already flowering, specially the those near to inoculated Trichoderma. This is nos surprising becasue Trichoderma have not colonized the roots, so this is not an effect of Trichoderma atroviride in plant and therefore in near ones.
*At the end of the day I will uncap the plants.
==Intergenic sequences in T.atroviride==
====Things to do====
*Run BLAST JGI.
*Chek BLASTX made by Martha with this sequences[http://openwetware.org/images/8/8b/IntergenicFasta.fna Whole Intergenic],[http://openwetware.org/images/8/85/IntergenicFasta480.fna 480bp away Intergenic],[http://openwetware.org/images/7/76/IntergenicFasta770.fna 770bp away Intergenic],[http://openwetware.org/images/d/dc/IntergenicFasta1020.fna 1020bp away Intergenic].
*Ask to Lizbeth for beans characteristics.
*Run BLAST for overlapped sequences in my PC.
====Things done====
*BLAST in JGI, done but useless for the lack of analysis sequences (just 100).
*Martha didn't come to the lab. She has flu.
*Run BLAST for overlappend sequences in my PC, is running. Specification below.
===Loogbook===
To run BLAST for overlappend sequences in my PC,I used the next parameters.


====Things done====
<code>
./blastn -db TrichodermaAtrovirideV2 -evalue 1e-5 -num_alignments 10 -query /home/fabricio/Desktop/GeneSiftWholeTables.Standardized/IntergenicOverlappedFasta.fas -out /home/fabricio/Desktop/GeneSiftWholeTables.Standardized/IntergenicOverlapped -word_size 6
</code>
Is still running.


===Intergenic sequences in T.atroviride===
===Intergenic sequences in T.atroviride===

Revision as of 11:57, 17 August 2012

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Trichoderma & A. thaliana interaction

Trichoderma & A. thaliana interaction

Things to do

  • Check plants
  • Uncap the plants

Things done

  • Check plants

Loogbook

  • When I went to see the plants, some of them were already flowering, specially the those near to inoculated Trichoderma. This is nos surprising becasue Trichoderma have not colonized the roots, so this is not an effect of Trichoderma atroviride in plant and therefore in near ones.
  • At the end of the day I will uncap the plants.

Intergenic sequences in T.atroviride

Things to do

Things done

  • BLAST in JGI, done but useless for the lack of analysis sequences (just 100).
  • Martha didn't come to the lab. She has flu.
  • Run BLAST for overlappend sequences in my PC, is running. Specification below.

Loogbook

To run BLAST for overlappend sequences in my PC,I used the next parameters.

./blastn -db TrichodermaAtrovirideV2 -evalue 1e-5 -num_alignments 10 -query /home/fabricio/Desktop/GeneSiftWholeTables.Standardized/IntergenicOverlappedFasta.fas -out /home/fabricio/Desktop/GeneSiftWholeTables.Standardized/IntergenicOverlapped -word_size 6 Is still running.

Intergenic sequences in T.atroviride

Things to do

Things done
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