User: lagartija
lagartija • 50
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Posts by lagartija
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... Hi,
I'm trying to make a database for rpsblast but I don't know how to create a pssm for the database. I have an alignment in fasta format : https://prosite.expasy.org/cgi-bin/aligner?psa=PS50104&format=FASTA
and I can also get more information about this domain on prosite : https://prosite.e ...
written 12 days ago by
lagartija • 50
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... Hi, I'm found this post useful because I have the same task (exept that I prefere to work on contigs than on bins). I also mapped the reads to my contigs to get the mean coverage. Is that a sufficient estimation of the (relative) abundance or do I have more steps to do to reduce biases ? ...
written 20 days ago by
lagartija • 50
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... Thank you for your answer. I think the default parameter is the fruit fly. Can I avoid orfing by augustus somehow ? ...
written 4 weeks ago by
lagartija • 50
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... Hi,
I'm trying to assess my genome completeness and possible contamination with busco. Is it possible to run it several files at the same time ? Is it also possible not to use a reference species when orfing with augustus while running BUSCO ?
I am trying to find an equivalent to checkm but for e ...
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... Hello everyone,
I have a question that might interest people making their own blast protein database. I see there is an option to mask low complexity regions with segmasker before (or after) making a database.
How useful is that for protein ? I see why it can really reduce false positives in nucl ...
written 7 weeks ago by
lagartija • 50
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... Thank you for this post ! I can't believe that something so elemental would be so complicated. ...
written 9 weeks ago by
lagartija • 50
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... I think you have an option like --merged but I don't remember. As said you should check the manual and you would propably find it because you can literally give any kind of data to spades. ...
written 9 weeks ago by
lagartija • 50
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... Hi everyone,
I'm currently starting in metagenomics and I would like to compare the overall functions present in different samples (I already have the sequences of the ORFs). Which method do you recommend for that ?
I came across Fun4me that looks like what I am looking for but nobody seems to u ...
written 9 weeks ago by
lagartija • 50
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Comment:
C: GenBank ID to GO term
... I have metagenomic data and I would like to have the GO terms to make a chart of the represented functions in my different samples ...
written 9 weeks ago by
lagartija • 50
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... Hi everyone,
I have a blast result from ref seq and I would like to have a quick overview of the functions present in my genomes. Do you know how I can get the GO terms from the NCBI accession number ?
I know I can do that with Blast2Go but I am looking for a free alternative.
Thank you in adva ...
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