User: ulises.rodriguez

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Posts by ulises.rodriguez

<prev • 9 results • page 1 of 1 • next >
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PAML ancestral sequences reconstruction
... Hello, I have a set of about 9,000 groups of orthologous proteins I'm trying to do ancestral sequence reconstructions for each of these groups based on their phylogenies, and then to compare each nucleotide position in a species of interest to the reconstructed sequences at key ancestral nodes. I ...
sequence alignment written 4 weeks ago by ulises.rodriguez0
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phylogenetics trees in r
... Good afternoon, I know that this blog is not precisely about phylogenetics subjects, but I'm stuck using **phylotools in R** , I'm trying to mapping a matrix which contains continue values in a phylogenetic tree. It seems that my tree has zero and negative edges lengths, and when I try to map the m ...
R written 10 weeks ago by ulises.rodriguez0
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(Closed) split text file in multiples text files
... Hello, I Have a file text that looks like this number1.1 characters_string_1 number1.2 characters_string_2 number1.3 characters_string_3 number2.1 characters_string_1 number2.2 characters_string_2 number2.3 characters_string_3 number3.1 character ...
sequence written 3 months ago by ulises.rodriguez0 • updated 3 months ago by anicet.ebou130
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change headers from fasta files
... I have multifasta files containing sequences like these: >16S_ribosomal_RNA attgcaggtcagcatactgcagtgaattcgttcc >16S_ribosomal_RNA attgcaggtcagcatactgcagtgaattcgttcc >16S_ribosomal_RNA attgcaggtcagcatactgcagtgaattcgttcc these sequences are contained in fas ...
sequence written 3 months ago by ulises.rodriguez0 • updated 3 months ago by cpad01129.0k
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extraction of the 16s rRNA gene from a file containing the genome
... Hello everyone, I have a fasta files containing genomes of bacterias and I would like to extract only 16s rRNA gene, I have tried with R packages like "micropan" with the function barrnap using the following code `barrnap(genome.file = "file_containing_genome.fasta",bacteria = T,cpu = 8)` and the o ...
genome gene sequence written 3 months ago by ulises.rodriguez0 • updated 3 months ago by sacha1.5k
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Comment: C: statistics data, observed vs expected values
... this is a sample of the data, I have approximately 3500 genomes https://i0000.clarodrive.com/s/oxfB4puIAmmrCrf ...
written 4 months ago by ulises.rodriguez0
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statistics data, observed vs expected values
... I have a data.frame () with the values of the observed and expected frequency of a kmer in multiples genomes, and I would like to obtain a threshold value to classify the genomes according to their observed and expected values. I have been trying with Chi-square test and G-test, but I'm not sure the ...
R written 4 months ago by ulises.rodriguez0 • updated 3 months ago by Biostar ♦♦ 20
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DNA-binding sites to proteins in bacteria
... is there a data base for all dna-binding sites to proteins for the bacteria domain? ...
sequence written 4 months ago by ulises.rodriguez0 • updated 4 months ago by Alex Reynolds25k
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headers from multifasta files
... I have a folder with multifasta files and I would like to extract the headers from each one of them, I've used the following command in shell grep -e ">" *.fasta > prueba_nc.txt the output looks like it Adenoviridae_genomas.fasta:>AC_000001 [AC_000001] Ovine adenovirus A, comp ...
sequence written 4 months ago by ulises.rodriguez0 • updated 4 months ago by Vijay Lakhujani3.0k

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