User: Petr Ponomarenko

gravatar for Petr Ponomarenko
Reputation:
1,550
Status:
Trusted
Location:
United States / Los Angeles / ALAPY.com
Website:
http://ALAPY.com/
Scholar ID:
Google Scholar Page
Last seen:
5 days, 1 hour ago
Joined:
2 years, 5 months ago
Email:
p*******@gmail.com

I am passionate about the prediction of changes in living creatures and populations due to mutations, epigenetics, lifestyle and environmental factors.

My first projects in bioinformatics were related to computation speed increase in algorithms like CE while I was in high school back in 2004. Later I got interested in protein-drug interactions, epitopes, MHC, 3d structures, modeling kinetics of different reactions under genetic variations and finally NGS.

You can reach me by writing to Petr at the website contact forms ALAPY.com

ALAPY provides data management and analysis services and makes free tools for the comunity, like our fastq lossless compression tool ALAPY Compressor and variant annotation and filtration tool (including trio analysis) ALAPY Genome Explorer. Please let us know about your ideas, questions and experience about data compression in this discussion: https://www.biostars.org/p/245423/

Posts by Petr Ponomarenko

<prev • 240 results • page 1 of 24 • next >
0
votes
3
answers
421
views
3
answers
Comment: C: NGS files' shrinkage software: ALAPY Compressor, only fastq files so far =)
... :) it is a server used for research by many people. Sure I told server owners and managers that storage is a big problem. ...
written 7 days ago by Petr Ponomarenko1.6k
0
votes
3
answers
421
views
3
answers
Comment: C: NGS files' shrinkage software: ALAPY Compressor, only fastq files so far =)
... Genomax2, you are right. I have very little amount of free space on one of our servers ...
written 7 days ago by Petr Ponomarenko1.6k
0
votes
3
answers
421
views
3
answers
Comment: C: NGS files' shrinkage software: ALAPY Compressor, only fastq files so far =)
... Dear Deepak Tanwar We had run a comparison of compression ratio, compression time and decompression time for xz. I know you are waiting for -3 and -9 results. While a big reply with benchmark explanation and software testing is in the works, we decided to start to publish some preliminary data. Res ...
written 7 days ago by Petr Ponomarenko1.6k
0
votes
3
answers
421
views
3
answers
Comment: C: NGS files' shrinkage software: ALAPY Compressor, only fastq files so far =)
... This is interesting. How would you store reads order? Because it affects alignment for paired end read experiments making results irreproducible if the original fastq files were discarded. How can I use it in clinical settings? I understand research projects potential ability to have something irrep ...
written 9 days ago by Petr Ponomarenko1.6k
0
votes
3
answers
421
views
3
answers
Comment: C: NGS files' shrinkage software: ALAPY Compressor, only fastq files so far =)
... I agree, but at the same time, I see doctors and researchers receiving hard drives over mail with terabytes of fastq, bam and vcf files to store and analyze. If sequencing prices are are going to continue to go down and amounts of data per sample will continue to grow up, I can imagine a moment wher ...
written 9 days ago by Petr Ponomarenko1.6k
0
votes
3
answers
421
views
3
answers
Comment: C: NGS files' shrinkage software: ALAPY Compressor, only fastq files so far =)
... Great. Thank you for the offer, WouterDeCoster. We like beer a lot =) ...
written 9 days ago by Petr Ponomarenko1.6k
0
votes
0
answers
101
views
0
answers
Comment: C: Get Get GC Content from UCSC with perl script (mysql)
... I am trying to understand your question. Is it as follows: How can I find nucleotide composition (GC content and such) of genomic regions from bed file using online tools that do not download the reference fasta file to my server/computer. Preferably using ucsc server for the computation. I believ ...
written 12 days ago by Petr Ponomarenko1.6k
0
votes
0
answers
115
views
0
answers
Comment: C: cuff merge does not run
... By any chance could you please share with us the files or at least parts of files that reproduce the problem? Is there any chance your reference is not the one used for the gtf? ...
written 12 days ago by Petr Ponomarenko1.6k
0
votes
1
answer
131
views
1
answers
Answer: A: Power of ADMXITURE mapping
... I am not sure what do you mean with ADMIXTRURE mapping, but whenever we use ADMIXTURE and admixture vectors for analysis we create our own statistic test that is based on these vectors as inputs. We have a set of true and mockup populations from around the world with known and modeled characteristic ...
written 13 days ago by Petr Ponomarenko1.6k
1
vote
2
answers
156
views
2
answers
Answer: A: How to find sequencing errors
... Reads do not show same nucleotides as what? Same as reference nucleotides at some positions? If for a given position you see 60% of reads have reference nucleotide and 40% have another nucleotide at this position, then it is very likely a heterozygous call if this is a diploid genome. There is a way ...
written 14 days ago by Petr Ponomarenko1.6k

Latest awards to Petr Ponomarenko

Appreciated 19 days ago, created a post with more than 5 votes. For A: How to sort VCF "chr1, chr2..."
Scholar 19 days ago, created an answer that has been accepted. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Scholar 19 days ago, created an answer that has been accepted. For A: find matching gene symbol
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Appreciated 22 days ago, created a post with more than 5 votes. For A: How to sort VCF "chr1, chr2..."
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Scholar 5 weeks ago, created an answer that has been accepted. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Scholar 6 weeks ago, created an answer that has been accepted. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: How to sort VCF "chr1, chr2..."
Supporter 6 weeks ago, voted at least 25 times.
Scholar 6 weeks ago, created an answer that has been accepted. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Guru 6 weeks ago, received more than 100 upvotes.
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Centurion 8 weeks ago, created 100 posts.
Scholar 8 weeks ago, created an answer that has been accepted. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: How to sort VCF "chr1, chr2..."
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: How to sort VCF "chr1, chr2..."
Scholar 9 weeks ago, created an answer that has been accepted. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Scholar 9 weeks ago, created an answer that has been accepted. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: isoforms and the definition of a protein

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1085 users visited in the last hour