User: Mathilde

gravatar for Mathilde
Mathilde0
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Denmark/Germany
Last seen:
2 years ago
Joined:
2 years, 4 months ago
Email:
d****@uni-greifswald.de

Posts by Mathilde

<prev • 10 results • page 1 of 1 • next >
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Comment: C: How to create an output file with sequence ID's from multiple BLAST result using
... Hi again, I tried to send it to you (on the 23rd of July) - but not sure if I send the files you asked for? - did you receive it? (it is not to rush you, just making sure if the email reached you)   Best, Mathilde ...
written 2.3 years ago by Mathilde0
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Comment: C: How to create an output file with sequence ID's from multiple BLAST result using
... No, I dont think so. I don't experience any problems with the network. I tried to run it many times during the day. Will be out of the office for a few days but will try again thursday. ...
written 2.3 years ago by Mathilde0
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Comment: C: How to create an output file with sequence ID's from multiple BLAST result using
... Again many thanks! - I am embarrassed to say I still can't get it to work... The error now is, when I try to run res = blastSequences(dna1, as="XML") I get: Error: failed to load HTTP resource I have tried to look up help here: ?htmlParse ?xmlToDataFrame But did not find any obvious solutions ...
written 2.4 years ago by Mathilde0
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Comment: C: How to create an output file with sequence ID's from multiple BLAST result using
... Thank you so much for the detailed answer. Your first advice worked, and I can get the "data.fame" output - perfect :) However the function blastSeqKK still only works when the fasta file contains only 2 sequences - more, and it gives the error of "no result after xx attempts" I have set the attem ...
written 2.4 years ago by Mathilde0
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Comment: C: How to create an output file with sequence ID's from multiple BLAST result using
... Thank you for you reply. However I am still struggling. the blastSequences() does not work for me. estimated response time 33 seconds elapsed time 35 seconds timeout after 61 seconds; wait another 60 seconds? [y/n] (I have pressed "y" many times and increased the timeout time to 320 sec) A pro ...
written 2.4 years ago by Mathilde0
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Comment: C: How to create an output file with sequence ID's from multiple BLAST result using
... No but the result "the list of ID for best hit" is not produced at the end of K.Keenan's "guide". I know what to do with it once I got the info :)   I have this now: [[1]] [[1]][[1]] DNAMultipleAlignment with 2 rows and 324 columns      aln [1] CTGAATCTGCGAACGGCTCCGCACACCAGTTGCAAA...GATGGCAGCGTA ...
written 2.4 years ago by Mathilde0
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How to create an output file with sequence ID's from multiple BLAST result using blastSequences in "Biostrings"
... Hello all, I don't have a problem with a specific command. My problem is that I am stuck. What I wish to do is this: I have a list of sequences (42 with a length of app. 300-500bp) in a fasta file. I want to BLAST these in NCBI (blastn) and get a list of top-hits corresponding to my list. (not v ...
annotation biostrings blast written 2.4 years ago by Mathilde0 • updated 2.4 years ago by Martin Morgan ♦♦ 20k
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Comment: C: could not find symbol "keepNA" in environment of the generic function
... So sorry I didn't see that myself! - Thanks again for replying I will try, however I did already try with 20 attempts but put it down to 5 - to make it faster as I was trying different changes to make it work. I will put the number of attempts up instead :)  ...
written 2.4 years ago by Mathilde0
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Comment: C: could not find symbol "keepNA" in environment of the generic function
... Thank you for replying :) So I fixed my first problem by updating R (thought I had done that, but turned out I hadn't). Now a new problem arises - same function. What I am trying to do is the BLAST my DNA seq via R using the package "Biostring" and this function here (by K. Keenan): http://rstudi ...
written 2.4 years ago by Mathilde0
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Answer: A: could not find symbol "keepNA" in environment of the generic function
... Hi, I am new in R and I get a similar error: Error in nchar(x, type = "bytes") :    could not find symbol "keepNA" in environment of the generic function When I try to follow the guideline scipt here:  http://rstudio-pubs-static.s3.amazonaws.com/12097_1352791b169f423f910d93222a4c2d85.html I tri ...
written 2.4 years ago by Mathilde0

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