User: fyfes

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fyfes20
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Posts by fyfes

<prev • 21 results • page 1 of 3 • next >
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Kraken taxonomy sublevels
... Hi, Could you please tell me what does Kraken taxonomy sublevel mean? My output in taxonomy column is sometimes P (phylum) or sometimes P1 or P2. Thank you ...
kraken taxonomy taxonom written 5 weeks ago by fyfes20
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can standalone OMA be used on protein fasta (not genome)
... Hi, I have a group of proteins that I want to analyse if they are related, do you know if OMA can perform on only protein fasta as input? I am getting an error that I have provided 0 genomes so I am guessing it needs genomes as input but maybe there is an option to change the input many thanks! ...
orthologs oma written 3 months ago by fyfes20 • updated 3 months ago by adrian.altenhoff660
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CARD ID to UNIPROT ID
... Hello, I have some IDs from CARD database which are in GenBank format: ADH03009.1 AAA03550.1 AAC44793.1 CCP42991.1 AAB41701.1 CAC32082.1 BAM16262.1 Is there a way to mapp them directly to Uniprot? I have already tried uniprot programatic acces and online mapepr but id does not work. Many thanks! ...
uniprot card written 4 months ago by fyfes20 • updated 4 months ago by Sej Modha4.7k
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Comment: C: clustal omega distance matrix option
... thank you ...
written 4 months ago by fyfes20
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clustal omega distance matrix option
... Hi, do you know maybe how to select kind of BLOSUM (30 or 60) matrix in clustal omega command? Now I have: clustalo -i FASTA --distmat-out=DISTMAT --full ...
clustal distancematrix written 4 months ago by fyfes20 • updated 4 months ago by RamRS30k
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Comment: C: DISTANCE MATRIX CLUSTALW
... Thanks for nothing. I have already solved my problem. ...
written 4 months ago by fyfes20
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Comment: C: DISTANCE MATRIX CLUSTALW
... what kind of effort ... I need to compute a distance matrix based on protein pairwise alignment using clustal. that's it. ...
written 4 months ago by fyfes20
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(Closed) DISTANCE MATRIX CLUSTALW
... Hi, could you please help me how to perform distance matrix (BLOSUM 60) for proteins in clustalw? ...
clustal distancematrix written 4 months ago by fyfes20
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What is KEGG BRITE ?
... Hi, I am downloading some pathways for bacteria from KEGG using Bioservices Python package and sometimes I get ko01057 which can be assigned to KEGG class and sometimes map07021 which cannot be assigned to CLASS and is BRITE hierarchy. What is the difference? thank you ...
metabolism pathways kegg written 5 months ago by fyfes20
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Comment: C: RMSD in R: HELP
... i am not sure as I am unable to find documentation on R algoritm. I just would like to know if my R script is correct ...
written 6 months ago by fyfes20

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