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Forum: Bioinformatics 12-08-2016, 07:16 AM
Replies: 3
Views: 2,273
Posted By fireLog2
Thanks for this recommendation. It seems like a...

Thanks for this recommendation. It seems like a good opportunity to start reviewing manuscripts, since you can select one specific for your knowledge.

However, I haven't heard about this...
Forum: Bioinformatics 12-08-2016, 05:33 AM
Replies: 11
Views: 8,315
Posted By fireLog2
A laptop wouldn't be suitable for most of the...

A laptop wouldn't be suitable for most of the bioinformatic task. It doesn't have the power to do complex and intensive calculations. Therefor, ssh to a cluster is the way to go.

As for the OS, I...
Forum: Bioinformatics 06-10-2014, 08:19 AM
Replies: 1
Views: 3,261
Posted By fireLog2
This error can occur if you didn't remove the old...

This error can occur if you didn't remove the old entries in your mysql database. If you re-add your similarSequences.txt in the same database, the entries will be double.

I'm not sure if the...
Forum: Bioinformatics 12-12-2013, 04:32 AM
Replies: 5
Views: 3,982
Posted By fireLog2
Thanks for the idea. Here is the result: If I...

Thanks for the idea. Here is the result:
If I use the same value for db_size for different blast-db, I get same evalues.

Now is the problem partially solved. :) Next time, I will set at the...
Forum: Bioinformatics 12-11-2013, 11:45 PM
Replies: 5
Views: 3,982
Posted By fireLog2
Thank you rhinoceros for helping. But I...

Thank you rhinoceros for helping.

But I already read that post and tried the cumulative length. In my example they are 13581 aminoacids in all 33 sequences. And with try and error I found that the...
Forum: Bioinformatics 12-11-2013, 07:56 AM
Replies: 5
Views: 3,982
Posted By fireLog2
BLASTp parameter -dbsize problems (blastall -z)

Hello all,
I'm stuck at a blastp problem. I want to use the parameter -dbsize to incrementally add sequences to a blast output. Same option is available in blastall with the parameter -z.

I did...
Forum: Bioinformatics 10-02-2013, 08:43 AM
Replies: 25
Views: 20,140
Posted By fireLog2
Thank you! I will give it a try...

Thank you! I will give it a try...
Forum: Bioinformatics 08-19-2013, 07:13 AM
Replies: 2
Views: 1,765
Posted By fireLog2
Thanks you for your fast answer! I will dig...

Thanks you for your fast answer!

I will dig further... I think I already have wise2 installed. But I didn't know that this can be used.
Forum: Bioinformatics 08-19-2013, 06:53 AM
Replies: 2
Views: 1,765
Posted By fireLog2
Is it possible to run PfamScan direct on DNA sequence?

Hello,
is it possible to run a local installed Pfam prediction (PfamScan) direct on DNA sequence?

There is a search field on the homepage to do so (http://pfam.sanger.ac.uk/search). But I...
Forum: Bioinformatics 07-29-2013, 04:22 AM
Replies: 1
Views: 1,753
Posted By fireLog2
You an assign the GO annotation, InterPro matches...

You an assign the GO annotation, InterPro matches or Pfam domains to each gene. After this you can find the most overlapping annotation for each group to get an idea for the function of the whole...
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