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question about masked sequences

question about masked sequences - Bioinformatics

question about masked sequences - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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Old 02-22-2010, 01:57 PM
Pipette Filler
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Default question about masked sequences



Hi everyone.

I need to compare some BACend sequences against contigs sequences. First i made the comparison without masking the BACend sequences and then I masked them for SSR and simple repeats.

When I masked the BACends no alignment was made. I compared the results with and without masking and found the alignments without masking didn't occur between SSR or simple repeats.

Then, I don't understand why the alignments between unmasked BACends and the contigs are not the same as alignments between masked BACends and contigs at the same e-value. I even used a less astringent e-value without success.

Can somebody explain what is happenning?
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Old 02-26-2010, 04:18 PM
Pipette Filler
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Default Re: question about masked sequences

Hi everyone!
I'm doing a statistical analysis of percentages of several proteins in proteome and transcriptome of a unique organism. I would like to know if proteome and transcriptome may be considered similar or not. Which statistical test is proper?? i.e I have a matrix of 12 rows and 2 columns (proteome and transcriptome) and for some organism I I would like to infer some relation between them.
Thanks a lot.
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Old 02-26-2010, 04:18 PM
Pipette Filler
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Default Re: question about masked sequences

sorry there's not the correct place!
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