User: camachofrancine

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Posts by camachofrancine

<prev • 37 results • page 1 of 4 • next >
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Comment: C: Query UniProt database with Mnemonic identifier
... Update: I was able to convert using http://www.uniprot.org/mapping/ from UniProtKB AC/ID to UniProtKB. This works, but would like to be able to implement some code. Thanks! ...
written 4 weeks ago by camachofrancine80
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Query UniProt database with Mnemonic identifier
... I have a list of UniProt Names, Mnemonic identifier of a UniProtKB entry. I am trying to query the UniProt database to retrieve the information of that entry that matches the mnemonic identifier and following filtering: Human taxa and Reviewed. Is there a way to do this in R? What I currently am doi ...
R uniprot written 4 weeks ago by camachofrancine80
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Retrieve sequences that generated a HMM profile
... Hi All, I have HMM profiles but the raw sequences or multiple sequence alignments are not available. I saw the tool `hmmemit`, but this randomly generates sequences that match a given profile HMM. I do not want random sequences. Is there a way to obtain sequences or multiple sequence alignment tha ...
hmmer written 4 months ago by camachofrancine80 • updated 4 months ago by Jean-Karim Heriche15k
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Comment: C: Help with CD-hit commands for DNA sequences
... Which version are you running? I am running 4.6 (built on Jul 29 2016) ...
written 15 months ago by camachofrancine80
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Comment: C: Help with CD-hit commands for DNA sequences
... I thought cdhit -est were not good for large sequences. My max is 71KB large. Is cdhit-est ok? ...
written 15 months ago by camachofrancine80
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Answer: A: Adding Fasta unique identifiers
... A simple way, is to just iterate through the fasta file using Python and add the headers to a dict, if you find a match while iterating to the key then you can just add another field. Something like this. from Bio import SeqIO import os fastadir = "" fastafile = "input.fa" ...
written 15 months ago by camachofrancine80
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Help with CD-hit commands for DNA sequences
... Hi, I want to use cd-hit to stringently cluster and remove redundant DNA sequences (~14,500 sequences). I was doing a blastn all vs all and filtering for 98% qcovsHSP and 98% percent identity. Then running a script to find out of all the matches to keep the longer sequences. However, I found cd-h ...
software cdhit written 15 months ago by camachofrancine80
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Comment: C: Parse hmm(er) profiles in R
... Another option I can think of is that with hmmsearch you can use different flags to save the results in a table. Which you could use R to parse and format the data how you intend to use it. --tblout : save parseable table of per-sequence hits to file --domtblout : save parseable ...
written 16 months ago by camachofrancine80
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Comment: C: Parse hmm(er) profiles in R
... Hi, I've had the same issue, but I ended up using python. https://www.biostars.org/p/118421/#202292 ...
written 16 months ago by camachofrancine80
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Answer: A: Continuously add lines to ggplot with for loop
... I finally solved the above question after staring at the computer. Using aes_string() made it work. for(i in 1:nrow(stool_polyketide_analysis_df_vfam)){ rowDF<-stool_polyketide_analysis_df_vfam[i,] dfstart <-rowDF$sstart dfend<-rowDF$send gPlot<-gPlot+geom_l ...
written 17 months ago by camachofrancine80

Latest awards to camachofrancine

Great Question 3 months ago, created a question with more than 5,000 views. For Conditionally merge columns using Pandas
Popular Question 3 months ago, created a question with more than 1,000 views. For Tabular fields of DIAMOND.m8 file
Scholar 12 months ago, created an answer that has been accepted. For A: Sublime Text 2: Output Error After I Installed Anaconda
Popular Question 13 months ago, created a question with more than 1,000 views. For Conditionally merge columns using Pandas
Popular Question 17 months ago, created a question with more than 1,000 views. For Conditionally merge columns using Pandas
Popular Question 21 months ago, created a question with more than 1,000 views. For parsing hammer 2.3.2 results using biopython
Popular Question 22 months ago, created a question with more than 1,000 views. For Bulk downloading IMG gene ID information
Scholar 22 months ago, created an answer that has been accepted. For A: Sublime Text 2: Output Error After I Installed Anaconda
Popular Question 23 months ago, created a question with more than 1,000 views. For parsing hammer 2.3.2 results using biopython
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Scholar 3.0 years ago, created an answer that has been accepted. For A: Sublime Text 2: Output Error After I Installed Anaconda

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