User: dllopezr

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dllopezr40
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Posts by dllopezr

<prev • 39 results • page 1 of 4 • next >
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Parallelization of Biopython proccess
... Hi! I am working parsing blast xml outputs with Biopython and for performance purposes, I want to parallelize the process. The code takes a large blast xml output, perform a calculation over the alignments and save the result in a SQL database The code is as follows: from Bio.Blast import NCB ...
parallelization biophython sql written 4 weeks ago by dllopezr40
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Comment: C: SQL configuration for sequence data
... Hi Pierre, do you have any recomendation for the use of longblob? I'm thinking in use VARCHAR(MAX) for my sequence instead of text becuause i read this have improvements in memory and retrieve, but longblob is new to me. For example, In some situations, I would like to tell SQL that select the 'DNA' ...
written 5 months ago by dllopezr40
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SQL configuration for sequence data
... Hi everyone I'm creating a database that will have a table for protein and dna sequence. I'm looking for advices for the config of this table in mysql in terms of the data type use (VARCHAR, TEXT, LONGTEXT) as well as the codification and collation for this table. Can you help me with that? Thank ...
protein sql dna written 5 months ago by dllopezr40 • updated 5 months ago by Pierre Lindenbaum124k
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Answer: A: Blast script over multiple databases
... I already do it Because my databases have this name structure: `T"x"P"x"_T"x"` when x is a 1 to 4 number I create all the strings and passed it in the blast command #!/bin/bash for T in `seq 1 4`; do for P in `seq 1 4`; do for t in ...
written 8 months ago by dllopezr40
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Comment: C: Blast script over multiple databases
... Hi Lieven When I say "aliases" I refer to the name of the blast database is not a file but a name that represents the files. Example: The makeblastdb produces 3 files with names: T1P1T0.nhr, T1P1T0.nsq and T1P1T0.nal, but the name of the blast database to pass to blastn script is only T1P1T0 with ...
written 8 months ago by dllopezr40
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Blast script over multiple databases
... Hi community I have a folder with multiple blast databases. I want to run blastn over all databases and produce one output for each database. I'm trying something like that for i in `find . -name 'name_of_database'`; do time blastn -db "$i" -query Sondas_100.fasta -out "$i".out -ou ...
multipledatabases script blastn written 8 months ago by dllopezr40
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BLAST filter by identity percentage and query cover
... Hi community! For the purpose of my work I need that the blast ouput don't show me the hits with 100% identity and 100% query coverage with the command -perc_identity 100 I obtain only the hits with 100% identity, but I want the opposite. I've try something like -perc_identity <100 but seems B ...
query cover identity percentage blast written 9 months ago by dllopezr40
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sorting columns by same values to do DEG analysis
... Hi community! I am working with metagenomic output from MG-RAST, but the columns don't match and I need to solve this before doing my DeSEQ analysis. The table is something like this GeneName Count GeneName Count GeneName Count GeneName Count GeneA x GeneB x GeneA x Ge ...
sorting columns differential expression written 12 months ago by dllopezr40 • updated 12 months ago by Fabio Marroni2.4k
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Comment: C: Mock Metagenome Gene Content
... Thanks for your Answer Nitin. The problem is that I don't want to find out the abundance of an organism, I want to count the abundance of some genes of interest. For example, how many time the gene "nifH" is present in the sample, for this purpose I need to know the organism that carry this gene, ho ...
written 12 months ago by dllopezr40
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Mock Metagenome Gene Content
... Hi, community! I need to work with a mock metagenome community for the optimization of the alignment parameters of a tool I've found this community: https://www.nature.com/articles/sdata201681, that is composed of 26 bacterial and archaeal genomes. For the purpose of my work I need to know the a ...
metagenome mock community gene content written 12 months ago by dllopezr40

Latest awards to dllopezr

Supporter 5 months ago, voted at least 25 times.
Popular Question 8 months ago, created a question with more than 1,000 views. For Command line tool for translated multifasta nucleotide to aminoacid sequence
Popular Question 8 months ago, created a question with more than 1,000 views. For How to include complete labels names in R boxplot
Scholar 8 months ago, created an answer that has been accepted. For A: Blast script over multiple databases

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