User: Petr Ponomarenko

gravatar for Petr Ponomarenko
Reputation:
2,500
Status:
Trusted
Location:
United States / Los Angeles / ALAPY.com
Website:
http://ALAPY.com/
Scholar ID:
Google Scholar Page
Last seen:
4 weeks, 1 day ago
Joined:
3 years, 7 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 • 304 results • page 1 of 31 • next >
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Comment: C: Peak calling with MACS for paired end DNase-seq data
... Could you please look at your two samples in parallel on IGV? Does it look that you are missing many peak? Could you please describe your experimental setup, wild type and mutant in more details? ...
written 6 weeks ago by Petr Ponomarenko2.5k
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Comment: C: Reliable Fastq compression programs
... Have you tried using compressed files with decompression in process substitution in Linux <(...) or read from stdin? fastqc <(decompress compressed.file) ...
written 10 months ago by Petr Ponomarenko2.5k
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Comment: C: Reliable Fastq compression programs
... Yannick, I am very interested too since we made our lossless compression algorithm https://www.biostars.org/p/245423 and we think it is worth mentioning. ...
written 10 months ago by Petr Ponomarenko2.5k
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Comment: C: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and
... Thank you Brian. We updated alapy.com website. Should work now. ...
written 10 months ago by Petr Ponomarenko2.5k
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Comment: C: Script to run blast locally with multiple files in a directory as queries
... Please refer to https://www.gnu.org/software/parallel/parallel_tutorial.html (wget -O - pi.dk/3 || curl pi.dk/3/ || \ fetch -o - http://pi.dk/3) | bash Usualy it is part of your dist and I have seen it on CentOS dist as well ...
written 11 months ago by Petr Ponomarenko2.5k
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Answer: A: Script to run blast locally with multiple files in a directory as queries
... I loe GNU parallel for such things. Something like ls *.fasta | parallel -a - blastp -query {} -db swissprot --out {.}.out since it allows to do it in parallel for many jobs ...
written 12 months ago by Petr Ponomarenko2.5k
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Answer: A: How to improve existing transcriptome annotation using cufflink protocol ?
... You might be able to improve annotation using dedicated software that can use transcriptome support as one of the evidence, plus add information about evolutionary related species genomes, genes, pram domains and so on. You can look at a variety of such tools likа maker, augustus, fgenesh, genemark ...
written 12 months ago by Petr Ponomarenko2.5k
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Comment: C: Restructuring table: rows to column and interleaving columns
... Please use real data in snipped then. Otherwise you and me just wasted a bit of our time. You can use for loop to collect and print the data. ...
written 12 months ago by Petr Ponomarenko2.5k
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Answer: A: How to remove lines with unmatched columns
... awk '{if(gsub(",","",$5)==gsub(",","",$6)){print $0}}' input.txt gsub returns number of substitutions it made ...
written 12 months ago by Petr Ponomarenko2.5k • updated 12 months ago by genomax49k
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Answer: A: Restructuring table: rows to column and interleaving columns
... awk 'FNR==1{id="ID";b4="B4";b3="B3"}FNR>1{id=id FS $1 FS $1;b4=b4 FS $2 FS $3;b3=b3 FS $4 FS $5}END{print id;print b4;print b3}' input.txt ...
written 12 months ago by Petr Ponomarenko2.5k

Latest awards to Petr Ponomarenko

Teacher 4 months 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?
Popular Question 12 months ago, created a question with more than 1,000 views. For Bioinformatics software distribution
Teacher 12 months 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 12 months ago, created an answer that has been accepted. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?
Popular Question 12 months ago, created a question with more than 1,000 views. For Lossless ALAPY Fastq Compressor (now with stdin/stdout support)
Scholar 12 months 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 13 months 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 13 months ago, created a post with more than 5 votes. For A: How to sort VCF "chr1, chr2..."
Teacher 13 months 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 13 months ago, created a comment with at least 3 up-votes. For C: NGS files' shrinkage software: ALAPY Compressor, only fastq files so far =)
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: isoforms and the definition of a protein
Appreciated 13 months ago, created a post with more than 5 votes. For A: Strore in separated fasta files fasta sequences with same locus
Teacher 13 months 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?
Voter 13 months ago, voted more than 100 times.
Scholar 13 months 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 13 months 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 13 months 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 14 months ago, created an answer that has been accepted. For A: find matching gene symbol
Scholar 14 months 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 14 months ago, created a post with more than 5 votes. For A: How to sort VCF "chr1, chr2..."
Teacher 14 months 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?
Teacher 14 months 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 14 months ago, created a post with more than 5 votes. For A: How to sort VCF "chr1, chr2..."
Scholar 15 months ago, created an answer that has been accepted. For A: How can I select my Chip-seq genes (targets) in my Rna-seq data?

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