User: ma23

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ma2340
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Posts by ma23

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Nanopore hybrid assembly
... Hi everyone! Can somebody please reccomend me any literature/tutorial or something for the nanopore hybrid assembly ? ...
next-gen nanopore sequencing written 7 months ago by ma2340
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DeNovo sequencing of proteins: Twister outputs an empty file.
... Hi all, Is there anybody who has used the Twister tool for de novo sequencing of proteins? I have just tried it on the sample I downloaded from here: https://www.ebi.ac.uk/pride/archive/projects/PXD003348, but the output file appeared to be empty. The raw file I converted to the mzXML format via ...
proteomics twister denovo written 8 months ago by ma2340
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De Novo Protein Sequencing. Tutorial for Dummies
... Hi everyone! I have the task of de novo protein sequencing: from the ms/ms spectra of protein proteolysis fragments by several proteases I have to obtain the sequences of possible variants of the protein struсture. In some cases, reference sequences may be available but basically no reference. I ...
proteomics denovo written 8 months ago by ma2340
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Answer: C: The NeedlemanWunsch alignment crashes on certain sequences
... Ok, I think I might have solved the problem. The peptide that causes the problem begins with a combination of acids 'ID'. So the command just takes it as a sign that the format of the input is embl. I've changed the call: needle plain::seq1.txt plain::seq2.txt -datafile EPAM30MS -gapopen 12 -g ...
written 8 months ago by ma2340
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Comment: C: The NeedlemanWunsch alignment crashes on certain sequences
... I've added -sprotein1 -sprotein2 but it didn't get better. So I assume the problem is something else. ...
written 8 months ago by ma2340
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Comment: C: The NeedlemanWunsch alignment crashes on certain sequences
... I execute the command as shown below: needle seq1.txt seq2.txt -datafile EPAM30MS -gapopen 12 -gapextend 2 output Each .txt contains only one line that is exactely the sequence. When one of txt presents the sequence 'IDMSAYPVESIR' the troubles begin. ...
written 8 months ago by ma2340 • updated 8 months ago by lieven.sterck8.0k
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The NeedlemanWunsch alignment crashes on certain sequences
... Hi all, I have two lists of sequences and I need to calculate the similarity for every pair from these two lists. So I apply 'needle' from EMBOSS package. Everything goes fine until this sequence comes across: 'IDMSAYPVESIR'. When it happens the program crashes with the message: Warning: Sequ ...
alignment emboss written 8 months ago by ma2340 • updated 8 months ago by Joe17k
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Is there any statistical test for comparison of two lists of proteins ?
... Hi all, I have two lists of proteins: one obtained from a healthy person's sample and the other - from a diseased one. Each protein has a score - a number that represents the degree of confidence that a protein really was represented in a sample. I want to make some kind of comparison between these ...
proteomics excel statistics written 9 months ago by ma2340 • updated 9 months ago by Asaf8.1k
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Comment: C: Capture gene name from NCBI for a protein accession
... No, it can't handle my file. ...
written 10 months ago by ma2340
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Capture gene name from NCBI for a protein accession
... Hi, I have a .csv file that contains a list of protein accessions. I need to add in every row the gene name that corresponds to each protein. I can make it by simple iteration by all proteins using a swiss-prot data base. But this method takes too much time. Are there any tools or libraries that c ...
ncbi python parse written 10 months ago by ma2340

Latest awards to ma23

Scholar 8 months ago, created an answer that has been accepted. For C: The NeedlemanWunsch alignment crashes on certain sequences

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