User: Neuls

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Neuls0
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Posts by Neuls

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Xscore Installation Issue using Bash
... It is not working, same error as before ...
written 11 weeks ago by Neuls0
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Comment: C: Xscore Installation Issue using Bash
... They are : -rw-r--r-- 1 marta marta 38801 mag 25 2016 RESIDUE_DEF_XTOOL. Is it a permission problem? ...
written 11 weeks ago by Neuls0
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Xscore Installation Issue using Bash
... Dear all, I am trying to install xscore v1.3 ([Xscore Manual][1]). They provide instructions to set up some environmental variables in the .cshrc file under C-shell. setenv XTOOL_HOME the_installation_directory_of_X-Score setenv XTOOL_PARAMETER $XTOOL_HOME/parameter setenv XTOOL_BI ...
installation csh c shell xscore bash written 11 weeks ago by Neuls0 • updated 7 weeks ago by John Marshall1.4k
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Protein flexibility B factor
... I was asked to search for epitopes in a protein and assess if they were flexible. To my knowledge i have mainly one possibility which would be doing MD and calculate the rmsf and rmsd for the region of insterest (I have no clue about time scale.. im short on computational power) However, i wonder i ...
protein flexibility b-factor written 7 months ago by Neuls0
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jModelTest - Interpreting its outputs
... Hi, I ran jModeltest program in order to choose the model that best fits my data using different selection criteria (AIC, BIC..). I'm having trouble to interpret one of the outputs given by this program: ![jModeltest Output][1] For one model of substitution the program takes a summary comparing wh ...
jmodeltest substitution model phylogenetics written 17 months ago by Neuls0
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How can I download all NR fasta sequences corresponting to the same specie from NCBI?
... Hi, I'm interested on comparing 16S rna among some species so I'd like to download all NR_ fasta sequences from NCBI 16Sdatabase corresponding to a specie of interest. I have been reading about Enterz but I wonder if it can be done easly from a webrowser. So far I got sequences from Silva database ...
ncbi 16s nr entrez written 20 months ago by Neuls0
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cd-hit redundancy removal
... I'm planing to use cd-hit to remove redundancy from a 16S mRNA dataset I have got in order to build a philogenetic tree using Phylip later on. Maybe it is a newbiew question but I wonder if i have to remove redundacy before or after doing MSA using MAFFT. Also I wonder if the output from cd-hit ca ...
cd-hit redundancy written 21 months ago by Neuls0 • updated 21 months ago by Biostar ♦♦ 20
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Comment: C: Phylogenetic Tree to compare my sequences to a database
... thank you, this indeed helped me :) ...
written 21 months ago by Neuls0
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Comment: C: Phylogenetic Tree to compare my sequences to a database
... Interesting paper indeed. what dou mean by substitution model? ...
written 21 months ago by Neuls0
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Comment: C: Phylogenetic Tree to compare my sequences to a database
... Oh ya I know Jalview!! I forgot it could remove redundancy. Anyhow, I have already tried to upload that sequences but sadly my PC cant handle so I think I need a better PC to perform this task ^^". Thank you for the advice I was pretty lost with phylogenetic trees! ...
written 21 months ago by Neuls0

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