User: Nickengland

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Nickengland130
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Posts by Nickengland

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Tool To Predict Deamidation Sites In A Protein
... I am looking for a tool to predict deamidation sites based on protein structure/sequence. I have found some papers which present the results of their method applied to a dataset, but no actual links to usable tools. Are there any, or do I need to code one based on the method described in the paper? ...
prediction protein written 7.3 years ago by Nickengland130 • updated 7.0 years ago by Biostar ♦♦ 20
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Comment: C: Strange Miseq Quality Issue, All "#" (Q2) After 100Bp On Read1, Read2 And Barcod
... I haven't directly, but the person who runs the sequencing facility has so we'll have to see what they say. ...
written 8.0 years ago by Nickengland130
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Strange Miseq Quality Issue, All "#" (Q2) After 100Bp On Read1, Read2 And Barcode Fine
... I had a sequence back recently with rather strange quality. For the forward read the fastQC graph shows after 100bp (150bp read) the quality drops to 2 for all samples. For the reverse read and the barcode the quality is fine. Looking at the sequences in the fastq shows they all end in a run of "#" ...
miseq written 8.0 years ago by Nickengland130 • updated 5.7 years ago by Biostar ♦♦ 20
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Biojava, Reason Indexes Are Inclusive One Based?
... In Biojava, and I assume other Bio* projects? Indexes for sequences positions using the standard API are 1-based inclusive rather than the more standard 0-based exclusive on the top end. This means if you are extracting a subsequence up to a certain number of leading bases which match something else ...
biojava written 8.2 years ago by Nickengland130 • updated 8.2 years ago by Istvan Albert ♦♦ 85k
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Tool To Generate Motif Diagrams
... I have seen diagrams for representing binding sites of proteins to DNA which shows 2 bases either side of the target site, with the vertical axis split into 4 different areas, A/C/T/G. The size of these letters corresponds to the ratio of that base in that position. A couple of different papers ha ...
motif dna written 8.4 years ago by Nickengland130 • updated 8.4 years ago by Neilfws49k
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Comment: C: Parse Blastdb Format From Java
... I'm doing some sequence mutation analysis from within Java, which uses blast to identify the closest matching genomic sequence. I have ~10million input sequences each run, but only ~200 static sequences in the blastDB to analyse. I could load the fasta files the blastDBs are generated from directly, ...
written 8.5 years ago by Nickengland130
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Parse Blastdb Format From Java
... Does anyone know a java library to parse blastDB files? I've found the specification at http://selab.janelia.org/people/farrarm/blastdbfmtv4/blastdbfmt.html for the file format, and the code for a C program to parse it, but not java library. The biojava API doesn't seem to have a class for it either ...
java blast written 8.5 years ago by Nickengland130
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Answer: A: Blast Database Sequences Length
... The length of the sequences is shown in the output. If you use XMLOutput it is there by default, if you use -outfmt 10 for csv format then you need to specify you want it with "slen" eg: -outfmt "10 std slen" see blastn --help for more options! ...
written 8.6 years ago by Nickengland130
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Comment: C: Loading Custom Genome In Igv Is Not Displaying Genes, Names Match.
... Very strange, if I just load the top line, with a huge start/end span, it loads perfectly. I suppose a binary search of the file is in order. ...
written 8.7 years ago by Nickengland130
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Comment: C: Loading Custom Genome In Igv Is Not Displaying Genes, Names Match.
... I've added the first few lines, the .fasta file starts ">test"\n ...
written 8.7 years ago by Nickengland130

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