User: Petr Ponomarenko

gravatar for Petr Ponomarenko
Reputation:
2,420
Status:
Trusted
Location:
United States / Los Angeles / ALAPY.com
Website:
http://ALAPY.com/
Scholar ID:
Google Scholar Page
Last seen:
5 days, 7 hours ago
Joined:
2 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 • 299 results • page 1 of 30 • next >
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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 8 days ago by Petr Ponomarenko2.4k
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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 8 days ago by Petr Ponomarenko2.4k
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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 days ago by Petr Ponomarenko2.4k
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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 13 days ago by Petr Ponomarenko2.4k • updated 11 days ago by genomax29k
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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 13 days ago by Petr Ponomarenko2.4k
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Comment: C: How to fix unmatched columns
... Dear BehMah. Could you please share with a few more lines of the original file and another snipped with desired result after data is fixed (make it manually). So we can understand exactly what you are looking for. Thank you. ...
written 13 days ago by Petr Ponomarenko2.4k
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Answer: A: compare two fasta files
... Install blastn https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download Run one file against the other (help is here https://www.ncbi.nlm.nih.gov/books/NBK279675/ or use blastn --help) blast -query file1.fasta -subject file2.fasta -outfmt 6 -out results.txt o ...
written 13 days ago by Petr Ponomarenko2.4k
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Comment: C: How to preform genome annotation?
... Yes, software parameters, genome annotation software uses different data like nucleotide composition at different features from nearby species and can use additional information from your organism, like transcriptome data. These datasets are used to adjust parameters in different statistical models ...
written 14 days ago by Petr Ponomarenko2.4k
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Comment: C: How to preform genome annotation?
... forgot about genemark, thank you ...
written 14 days ago by Petr Ponomarenko2.4k
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146
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Answer: A: How to preform genome annotation?
... We use http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=gfind Also we used MAKER http://www.yandell-lab.org/software/maker.html and Augustus http://bioinf.uni-greifswald.de/augustus/ You may use BUSCO http://busco.ezlab.org to assess quality. Also it is not that mu ...
written 15 days ago by Petr Ponomarenko2.4k

Latest awards to Petr Ponomarenko

Scholar 12 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?
Popular Question 14 days ago, created a question with more than 1,000 views. For Lossless ALAPY Fastq Compressor (now with stdin/stdout support)
Scholar 15 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?
Teacher 28 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?
Commentator 29 days ago, created a comment with at least 3 up-votes. For C: isoforms and the definition of a protein
Appreciated 29 days ago, created a post with more than 5 votes. For A: Strore in separated fasta files fasta sequences with same locus
Appreciated 29 days ago, created a post with more than 5 votes. For A: How to sort VCF "chr1, chr2..."
Teacher 29 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?
Commentator 29 days ago, created a comment with at least 3 up-votes. For C: NGS files' shrinkage software: ALAPY Compressor, only fastq files so far =)
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?
Voter 5 weeks ago, voted more than 100 times.
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?
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 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 10 weeks ago, created a post with more than 5 votes. For A: How to sort VCF "chr1, chr2..."
Teacher 10 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 10 weeks ago, created an answer that has been accepted. For A: find matching gene symbol
Scholar 10 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 11 weeks ago, created a post with more than 5 votes. For A: How to sort VCF "chr1, chr2..."
Teacher 11 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?
Teacher 3 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 3 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 3 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 3 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 3 months ago, created a post with more than 5 votes. For A: How to sort VCF "chr1, chr2..."

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