User: Alper Yilmaz

gravatar for Alper Yilmaz
Alper Yilmaz90
Reputation:
90
Status:
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Location:
Turkey
Website:
http://alperyilmaz.org...
Twitter:
alperyilmaz
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Google Scholar Page
Last seen:
3 years, 3 months ago
Joined:
9 years, 2 months ago
Email:
a**********@gmail.com

A bioinformatician in love with Linux..

Posts by Alper Yilmaz

<prev • 8 results • page 1 of 1 • next >
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Answer: A: blast -F F equivalent in blast+
... Seconds later I posted the question I noticed my mistake, I was supposed to test "-dust no" . When I use "-dust no" filtering is off. ...
written 6.0 years ago by Alper Yilmaz90
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blast -F F equivalent in blast+
... In legacy blast there is an option -F, which turns on or off filtering. By default filtering is ON and it effects my results a lot, so I turn it off by -F F (false) In blast+ I couldn't figure out the equivalent of -F F. In another post  it was suggested to use "-dust yes", I tried it and it does n ...
ncbi blast blast+ written 6.0 years ago by Alper Yilmaz90
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Metal Affinity Prediction Software
... I have many PDB files and would like to calculate affinity prediction of a particular metal ion (in kcal/mol) for each of them. Can you suggest a software suitable for my purpose? Thanks. (1)I tried FoldX and had very hard time working with it. (2) I posted a question earlier which was much broad ...
protein-structure written 6.5 years ago by Alper Yilmaz90
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Improved Metal Binding Upon Amino Acid Change
... Hi, I am trying to screen amino acid changes in a given protein and calculate if ligand binding has improved or not. I was searching for software for this purpose. In another post, it was suggested to use Modeller, Chimera or scwrl4. As far as I understand, these homolgy modeling software are able t ...
modeling protein-structure written 6.9 years ago by Alper Yilmaz90
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Retrieving Individual Genomes From 1000Genomes Project
... Hi all.. I was interested in retrieving individual genomes as fasta files from 1000genomes project. After some search I noticed that, the reference genome is available, individual sequencing reads (fastq format) are available, variant calls are available but individual assembled genomes are not avai ...
genome 1000genomes written 7.0 years ago by Alper Yilmaz90 • updated 7.0 years ago by zam.iqbal.genome1.7k
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Answer: A: Peak Detection In Intergenic Regions In Rna-Seq Data
... The question is already answered but still I wanted to offer an alternative for whomever reached this page for his/her needs. The USeq software, which was designed for ChIP-Seq initially, can be used for determining regions that are enriched in RNA-Seq as well. This might eliminate the arbitrary cut ...
written 9.0 years ago by Alper Yilmaz90
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Easy Way To Map Cds Coordinates To Genomic Coordinates
... Suppose that I have a protein domain in my GeneA, and I know coordinates of the domain within the cds sequence of GeneA. In addition, I know the genomic coordinates of GeneA (eg, in GFF format) along with mRNA, exon coordinates. Is there a easy way, to map the protein domain coordinates to genomic ...
cds gff coordinates mapping bed written 9.1 years ago by Alper Yilmaz90 • updated 9 weeks ago by Shicheng Guo8.1k
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Comment: C: What Are The Advantages/Disadvantages Of One-Based Vs. Zero-Based Genome Coordin
... the problem is, regarding widely used formats, BED and GFF, one can just use columns 4 and 5 in GFF file to generate a BED file and then coordinates will be shifted one basepair. An easy to make mistake! ...
written 9.1 years ago by Alper Yilmaz90

Latest awards to Alper Yilmaz

Popular Question 4.9 years ago, created a question with more than 1,000 views. For Easy Way To Map Cds Coordinates To Genomic Coordinates
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Easy Way To Map Cds Coordinates To Genomic Coordinates

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