User: Petr Ponomarenko

Reputation:
700
Status:
Trusted
Location:
United States/Los Angeles/ALAPY
Website:
http://alapy.com/
Scholar ID:
Google Scholar Page
Last seen:
2 hours ago
Joined:
2 years, 3 months ago
Email:
p*******@gmail.com

I am passionate about modeling minor changes in objects and processes of molecular biology. 

My first works were related to computation speed increase and databases like CE http://source.rcsb.org/jfatcatserver/ceHome.jsp back in 2004 while I was in high school. 

Later I learned about 3D structure modeling and small molecule docking at Ryben's Abagyan lab at The Scripps Research Institute.

Currently, my main interest is in SNPs analysis, Next Generation Sequencing and mathematical modeling.

Posts by Petr Ponomarenko

<prev • 98 results • page 1 of 10 • next >
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Comment: C: Why some questions in OPEN section of the Biostars.org have "(Closed)" at the be
... I get it. "(Closed)" appears together with the words in "The thread is closed. No new answers may be added." below the conversation. But my question is not technical at all. I am trying to understand the reasoning behind such classification of "(Closed)" questions as OPEN. ...
written 18 hours ago by Petr Ponomarenko700
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Forum: Why some questions in OPEN section of the Biostars.org have "(Closed)" at the beginning of the question?
... I am a little bit confused why adding new answers is not possible for questions that have "(Closed)" in the Post Title. Comments are available in such posts. Despite all this such question appear in the list of OPEN questions on Biostars. As a result, there are thousands of "(Closed)" questions in ...
biostars forum written 18 hours ago by Petr Ponomarenko700 • updated 12 hours ago by genomax222k
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Answer: A: resno fields within a pdb file
... I do not know of such a rule in pdb file format specification ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf . Information about some atoms or residues can be missing and if so there is a section in remarks describing what exactly is missing with some comments like why it is m ...
written 18 hours ago by Petr Ponomarenko700
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Answer: A: In GATK, SNPs and INDELs are called separately or together?
... It depends on what you are using GATK for and what you are using in GATK package for variant calling. For example, HaplotypeCaller is trying to find haplotypes likelihoods and uses these to find genotype likelihoods. https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadin ...
written 18 hours ago by Petr Ponomarenko700
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Comment: C: gff file name replace!
... There are buttons on top of the area you are typing your answer in. These are for formatting. One of the buttons has 1s and 0s in it. This is to provide samples of the code (and is good to show stdout output to the terminal). Here is your text formatted "Hi Petr, Thanks. My gff file is: Con ...
written 19 hours ago by Petr Ponomarenko700
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Comment: C: gff file name replace!
... Could you please format your text? Only to clarify before writing the answer, do you want to change Name=Contig11434.9 to Name=SGH012586-RA for genes and mRNAs and that is it? Anything else? (changes to gff file might affect the way other programs interpret It) ...
written 22 hours ago by Petr Ponomarenko700
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Comment: C: What is the fastest way to add 'Ns' to variable length sequences in a .fasta suc
... $ awk '$1~">"{name=$0}$1!~">"{for(i=1;i<=25000;i++){print name; print $0}}' your_file.fasta > your_100k.fasta $ wc -l your_100k.fasta 200000 your_100k.fasta $ time awk '$1~">"{print $0}$1!~">"{tmp="";for(i=1;i<150-length($0)+1;i++){tmp=tmp"N"};print $0""tmp}' ...
written 1 day ago by Petr Ponomarenko700
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Answer: A: PDB files: Valence error
... I have not used rdkit.Chem and do not know what sanitization means with it, but from my experience PDB structures require a lot of corrections including changes in charges (hydrogen atoms can not be seen in X-ray and at least with common equipment, also oxygen atom connected to residue or as part of ...
written 1 day ago by Petr Ponomarenko700
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Answer: A: Can I merge fastq files of a same sample from two sequencers for gene expression
... No, especially if it is paired end experiment and you are aligning to the transcriptome. The best way is to merge as late (downstream) as possible, because within each pair you have different distributions and thus different parameters for statistical models that are being used in almost every step ...
written 1 day ago by Petr Ponomarenko700
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Comment: C: What is the fastest way to add 'Ns' to variable length sequences in a .fasta suc
... and from my experience of teaching and giving workshops on different topics in bioinformatics students with no programming experience are ok with learning basic Unix programs and commands like grep and sort, while learning to write a simple program in R, ruby, python or java is much much harder, esp ...
written 1 day ago by Petr Ponomarenko700

Latest awards to Petr Ponomarenko

Appreciated 2 days ago, created a post with more than 5 votes. For A: How to sort VCF "chr1, chr2..."
Good Answer 2 days ago, created an answer that was upvoted at least 5 times. For A: How to sort VCF "chr1, chr2..."
Scholar 2 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 5 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 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 5 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 6 days ago, created a comment with at least 3 up-votes. For C: isoforms and the definition of a protein
Teacher 6 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 7 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 8 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 9 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 9 days ago, created an answer that has been accepted. For A: find matching gene symbol
Teacher 9 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 10 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 11 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 14 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 14 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 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 15 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?
Autobiographer 17 days ago, has more than 80 characters in the information field of the user's profile.

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