User: Tim

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Tim110
Reputation:
110
Status:
Trusted
Location:
United Kingdom
Last seen:
17 hours ago
Joined:
3 years, 10 months ago
Email:
t****************@gmail.com

Posts by Tim

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Whole-genome alignment of two or more bacterial genomes - find structural varian
... Thank you for recommending [NucDiff][1], it does exactly what I wanted. [1]: https://github.com/uio-cels/NucDiff "NucDiff" ...
written 9 days ago by Tim110
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Comment: C: Whole-genome alignment of two or more bacterial genomes - find structural varian
... Olson ND, Lund SP, Colman RE, et al. Best practices for evaluating single nucleotide variant calling methods for microbial genomics. Frontiers in Genetics. 2015;6:235. doi:10.3389/fgene.2015.00235. > **Calling SNPs using a genome assembly** > > SNPs can be identified from genome assemblie ...
written 12 days ago by Tim110
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Comment: C: Whole-genome alignment of two or more bacterial genomes - find structural varian
... NucDiff looks interesting for sure, will give it a go, thanks. ...
written 15 days ago by Tim110
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Comment: C: Whole-genome alignment of two or more bacterial genomes - find structural varian
... Thanks, haven't heard about it, will check later. ...
written 15 days ago by Tim110
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Whole-genome alignment of two or more bacterial genomes - find structural variants
... Hello, Let's say I have two or more complete bacterial genome sequences produced by Sanger sequencing and/or Nanopore/PacBio (no Illumina reads). The bacterial genomes in question are 95-99% identical on the nucleotide level. What would be the best way to align these genomes (with a pair-wise or mu ...
whole-genome alignment snp structural variant written 16 days ago by Tim110
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Answer: A: What can be done to compare several samples (1000 items) of tuberculosis whole g
... I guess you want to do something similar to what is described in this paper: [Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome][1] [1]: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122979 ...
written 11 months ago by Tim110
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Comment: C: Could someone suggest a fast and efficient implementation of a glocal (semi-glob
... Thanks, I will check it. ...
written 11 months ago by Tim110
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Comment: C: Could someone suggest a fast and efficient implementation of a glocal (semi-glob
... Thanks, I have checked Shuffle-LAGAN, seems to be a good program and I will test it later. My only concern is that was designed to do glocal alignments of long DNA sequences, while I have short-medium protein sequences (20-500 aa long). ...
written 11 months ago by Tim110
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Comment: C: Could someone suggest a fast and efficient implementation of a glocal (semi-glob
... Please correct me if I am wrong, but I had an impression that nucmer performs global alignments of long sequences, while I need semiglobal (glocal) alignments of short to moderately long sequences. I updated my original post to reflect the difference between different methods of alignment. ...
written 11 months ago by Tim110
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Could someone suggest a fast and efficient implementation of a glocal (semi-global) sequence aligner?
... I am looking for a program that would be able to perform semi-global (global in query, local in reference sequence) protein alignments fast and efficiently. My query sequences are short (20-30 aa), while reference sequences 10-20 times longer. So far I have been able to find [GLSEARCH][1] (from FAST ...
alignment protein glocal semi-global written 11 months ago by Tim110

Latest awards to Tim

Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Tools For Metagenomic Data Analysis
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Tools For Metagenomic Data Analysis
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Relative abundance (evenness) estimation/prediction in metagenomic datasets
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Tools For Metagenomic Data Analysis

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