Tutorial 1 - Coccidia.icb.usp.br
Tutorial 1 - Coccidia.icb.usp.br
Tutorial 1 - Coccidia.icb.usp.br
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9<<strong>br</strong> />
seed type: Protein<<strong>br</strong> />
#### Round 1 ####<<strong>br</strong> />
Total # of reads for CAP3: 4<<strong>br</strong> />
Length of the seed-contig C_jejuni: 755<<strong>br</strong> />
Accumulative number of reads: 4<<strong>br</strong> />
#### Round 2 ####<<strong>br</strong> />
Total # of reads for CAP3: 15<<strong>br</strong> />
Length of the seed-contig C_jejuni: 1739<<strong>br</strong> />
Accumulative number of reads: 19<<strong>br</strong> />
#### Round 3 ####<<strong>br</strong> />
Total # of reads for CAP3: 13<<strong>br</strong> />
Length of the seed-contig C_jejuni: 2813<<strong>br</strong> />
Accumulative number of reads: 32<<strong>br</strong> />
#### Round 4 ####<<strong>br</strong> />
Total # of reads for CAP3: 22<<strong>br</strong> />
Length of the seed-contig C_jejuni: 3756<<strong>br</strong> />
Accumulative number of reads: 54<<strong>br</strong> />
#### Round 5 ####<<strong>br</strong> />
Total # of reads for CAP3: 13<<strong>br</strong> />
Length of the seed-contig C_jejuni: 4928<<strong>br</strong> />
Accumulative number of reads: 67<<strong>br</strong> />
#### Round 6 ####<<strong>br</strong> />
Total # of reads for CAP3: 21<<strong>br</strong> />
Length of the seed-contig C_jejuni: 5733<<strong>br</strong> />
Accumulative number of reads: 88<<strong>br</strong> />
A contig reached the maximum number of bases!<<strong>br</strong> />
#### Last Round ####<<strong>br</strong> />
Length of the final seed-positive contig C_jejuni: 5732<<strong>br</strong> />
8. Running GenSeed with a protein sequence seed<<strong>br</strong> />
This time we will run GenSeed against the same database, but using a protein<<strong>br</strong> />
sequence seed of the same GAPDH gene. To run GenSeed, first go to the<<strong>br</strong> />
/tutorial_1/test directory, and then type the following command:<<strong>br</strong> />
genseed.pl –s ../seed/GAPDH_prot_seed.fasta –d ../db/CJ_shotgun.dbs<<strong>br</strong> />
-o output_prot -r 5<<strong>br</strong> />
You should now find a newly created output_prot subdirectory.<<strong>br</strong> />
Start inspecting the log file (genseed.log). You will see that GenSeed has<<strong>br</strong> />
appended new information on the previously existing file. This new information should<<strong>br</strong> />
like as follows: