User: Michael G

gravatar for Michael G
Michael G50
Reputation:
50
Status:
New User
Location:
Germany
Last seen:
1 week, 3 days ago
Joined:
5 years, 2 months ago
Email:
m*************@gmail.com

Posts by Michael G

<prev • 22 results • page 1 of 3 • next >
0
votes
1
answer
481
views
1
answers
Answer: A: extract annotation for mVISTA whole genome comparison
... I have written a blog post about how to set up a custom annotation file for the visualization of several genomes via mVISTA. The post includes an example using the plastid genome of Arabidopsis thaliana (i.e., is accessible to everyone via NCBI GenBank). You can find that post here: https://blogs. ...
written 10 days ago by Michael G50
1
vote
2
answers
1.5k
views
2
answers
Answer: A: VISTA annotation file
... I have written a blog post about how to set up a custom annotation file for the visualization of several genomes via mVISTA. The post includes an example using the plastid genome of Arabidopsis thaliana (i.e., is accessible to everyone via NCBI GenBank). You can find that post here: https://blogs. ...
written 10 days ago by Michael G50
0
votes
1
answer
151
views
1
answers
Answer: A: Visualizing nucleotide differences across aligned bacterial genomes
... I believe that [DNAPlotter][1] (which is part of the Artemis package) may be a tool for your purpose. The [installation instructions][2] for DNAPlotter are very straightforward, and there are plenty of [example visualizations][3] online to understand the capabilities of the software. The original pu ...
written 4 months ago by Michael G50
0
votes
1
answer
1.2k
views
1
answers
Answer: A: Commandline alternatives for generating EMBL flat files from NEXUS alignments
... I eventually wrote a software for that particular purpose: [annonex2embl][1] [1]: https://doi.org/10.1093/bioinformatics/btaa209 ...
written 4 months ago by Michael G50
0
votes
1
answer
151
views
1
answers
Comment: C: Visualizing nucleotide differences across aligned bacterial genomes
... That's a good question. I have also wondered about an appropriate visualization tool for such cases but not found a suitable solution yet. ...
written 4 months ago by Michael G50
3
votes
2
answers
703
views
2
answers
Answer: A: Printable visualizations of large-scale alignments
... I found that I can achieve what I was looking for using the command-line alignment viewer [alv][1]. It may not be super pretty, but it is fast: alv myReallyLargeAlignment.fasta -t dna -k -w 300 | aha | wkhtmltopdf - soughtVisualization.pdf In addition, the alignment viewer `belvu` of the [SeqT ...
written 23 months ago by Michael G50
0
votes
2
answers
703
views
2
answers
Comment: C: Printable visualizations of large-scale alignments
... @jrj.healey Theoretically I would agree, but a compilation of a texshade section (with 150000+ bp) in a LaTeX document would take ages. I am looking for something more light-weight. ...
written 23 months ago by Michael G50
0
votes
2
answers
703
views
2
answers
Comment: C: Printable visualizations of large-scale alignments
... @thackl The R-Package `msa` has been among my earlier tryouts, but is not a workable solution. It stalls when given a multi-sequence alignment of 20 or more bacterial genomes. Likewise, tex-documents with texshade-sections would take ages to compile (if at all) under such input alignments. In my exp ...
written 23 months ago by Michael G50
3
votes
2
answers
703
views
2
answers
Printable visualizations of large-scale alignments
... I would like to visualize a **large** ("large" as in 20 bacterial genomes) multi-sequence alignment such that (a) the sequences are wrapped within pages, (b) the individual nucleotide letters remain visible (at least minutely), and (c) nucleotide differences compared to a consensus are highlighted. ...
alignment sequence written 23 months ago by Michael G50
0
votes
0
answers
529
views
0
answers
Removing unmatched Ns from query sequence based on alignment
... Assume a contig of draft genome assembly that contains several regions of unknown sequence and length, which are indicated by stretches of 'N'. Further assume the presence of a contig of the same genome region, whose source is a complete and trustworthy genome assembly of the same organism. Finally, ...
genome alignment contig sequence written 2.5 years ago by Michael G50

Latest awards to Michael G

Popular Question 20 months ago, created a question with more than 1,000 views. For Commandline alternatives for generating EMBL flat files from NEXUS alignments
Popular Question 20 months ago, created a question with more than 1,000 views. For 2016 tool - native SOLiD (.csfasta and _QV.qual) to colorspace-encoded FastQ
Popular Question 20 months ago, created a question with more than 1,000 views. For Uploading data files to Webin upload area under Linux
Popular Question 20 months ago, created a question with more than 1,000 views. For Running samtools mpileup on BAM that contains colorspace
Scholar 23 months ago, created an answer that has been accepted. For A: 2016 tool - native SOLiD (.csfasta and _QV.qual) to colorspace-encoded FastQ
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Printable visualizations of large-scale alignments
Scholar 4.2 years ago, created an answer that has been accepted. For A: 2016 tool - native SOLiD (.csfasta and _QV.qual) to colorspace-encoded FastQ

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1574 users visited in the last hour