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Old 04-08-2010, 05:27 PM   #1
edge
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Location: China

Join Date: Sep 2009
Posts: 199
Default Genewise program output file discussion

Does anybody familiar with genewise program and know how to save the Genewise program output file into a new file?
I got two input file now:
1. A single dna fasta sequence of genome.fasta.masked (output file of RepeatMasker program)
2. Unitprot.fasta (protein database without formatted, in fasta format)

My purpose is wanted to run my genome.fasta.masked sequence against the unitprot fasta. Whether I needed to format my unitprot.fasta file by using NCBI "formatdb" before running the genewise program?
In my case, whether "genewise" or "genewisedb" more suitable to use to map my genome.fasta.masked sequence against the unitprot.fasta database?
Besides that, how I can save the output result of genewise program?
Command that I have tried:
/genewise/wise2.2.0/src/bin/genewisedb -prodb unitprot.fasta -dnas genome.fasta.masked -gff > output_result.gff
I plan to output the genewise program in gff format then save it to a file called (output_result.gff)
Thanks.
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