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Name: Sandro Valenzuela

Type: User

Sandro Valenzuela's Projects

16s18sits

16S pipeline based on dada2 including analysis and reports

automodeller

autoMod is a wrapper for all steps in homology modeling using modeller and their "ready to use" files

extractseq

Giving a contig name and positions (start and end), extractSeq can return the corresponding sequence from your fasta.

fetchmylineage

Giving genus and specie name, the script give you a complete lineage

gets2

getS2 calculate the order parameter for your protein (or range of residues), and you'll get a file like a format "reside value"

humanmicrobiomeanalysis

R Shiny application accompanying the paper (unpublished) Evaluation of Computational Methods for Human Microbiome Analysis Using Simulated Data

multigenomiccontext

multiGenomicContext is a pipeline to see your protein in many genomic context as much as gbk you have.

pastetaxid

This script take your fastas, search for common IDs (ti, acc, gi, gb, emb), get the taxID (or other ID if is missing), and finally create a new fasta with the new entries.

pathoscope2biom

an script for convert pathoscope2 output in biom format

plotmygbk

Plot your gbk in an standard circular plot.

remove my sequence is tool where you can remove a subsequence from your target sequence, it means giving a protein sequence, the tool will search for the corresponding match on your fasta target and then remove the match.

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