User: Izal

gravatar for Izal
Izal10
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10
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New User
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6 months, 4 weeks ago
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1 year, 11 months ago
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Posts by Izal

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Comment: C: InParanoid blast-all & formatdb Error
... You're absolutely right! :-P Okay, I've managed to fix the problem! In case someone else has the same problem, the solution is to simplify the sequence header. To solve this, it is necessary to edit the headers of the fasta file by simplifying them, eliminating any symbol or description of the sequ ...
written 6 months ago by Izal10
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InParanoid blast-all & formatdb Error
... Hi everyone! I'm trying to find protein orthologs between strains using InParanoid. But when I execute it, I obtain errors. **Is this normal? Or am I doing something wrong?** The command seems simple... Thanks in advance!!! **Command:** $ perl inparanoid.pl strain1.fa strain2.fa **Here, a ...
inparanoid ortholog formatdb blastall written 6 months ago by Izal10
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InParanoid: score and cut off for indentify orthologs
... Hi everyone, I am using InParanoid software for identify orthologs genes between strains of one specie. So, I expect to find very similar genes shared into both genomes. In a typical reciprocal blast, I set the cut off with and E-Value of 1e-7 and a %identity (pident) of 85%. However, InParanoid ...
orthologs inparanoid blast score written 8 months ago by Izal10
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How to convert SBML level 3 into SBML level 2
... Hi everyone! I have a SBML model file downloaded from a database, and when I open it in edit mode the file indicates that is level 3 SBML. Is there any way/tool to convert it to SBML level 2? (to use it with old software) Thanks a lot in advance! ...
bigg model modelling sbml reconstruction written 9 months ago by Izal10 • updated 9 months ago by mhucka0
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Reciprocal Blast & Parse best hits
... Hi everyone, I'm novice doing reciprocal blast and I have spent a lot of time trying it. I don't know how to do a reciprocal blast and how to parse the best hits and compare & find matches. So, an advice would be a big help to me. I need to do a reciprocal Blast in Python (Jupyter) to identi ...
reciprocal best hit blast parse written 10 months ago by Izal10

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