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Questions related to Bioinformatics and Computational Biology
I want to to do Synteny Mapping of some plant genes. SyMAP supports only Linux or McOSX. I need tool or software that runs on Windows OS
01 January 2017 1,031 3 View
Hi all, I am learning a lot of things about the computational biology for the first time. I was curious, with the current technology, what is the possible simulation time range for a research in...
01 January 2017 3,345 5 View
I want to use the output of the GBlock program for further processing in FastTree program. But the FastTree doesnt accept the output file resulting from Gblocking. Please provide me some suggestions!
01 January 2017 695 2 View
I have been stuck on this one for a while as it seems available tools are more concentrated on enrichment and differential expression at pathway level. I am however interested in understanding if...
01 January 2017 7,970 4 View
Hello, I want to sequence rRNA16S of bacteria by means of next generation sequencing technic using Illumina MiSeq technology. In articles i see that they choose hypervariable region V4 or V6...
22 December 2016 4,978 1 View
Hello, is there any user-friendly, publicly available resource to generate a phylogenetic tree from an ANI distance matrix? Thanks a lot, Ralf
21 December 2016 3,279 4 View
Hi! I was wondering if you can suggest program/script for linux or not, that can calculate the interactions between Ligand and protein from a pdb file. When I'm saying interactions i mean,...
20 December 2016 6,394 2 View
I have number of peptide structures. I want to calculate the number of active rotatable bonds in those peptides. I am looking for script or any software which calculates it.
19 December 2016 4,168 3 View
for protiens
12 December 2016 6,616 23 View
I have a list of selected SNPs in which I am interested for genotyping. The conducting company needs the flanking sequence of each SNP ? How do I get this or how can I download it from NCBI Gene...
12 December 2016 7,557 7 View
In the file all the column has gene expression data. I couldn't understand what those values are.
12 December 2016 7,080 4 View
Please recommend any free NGS data analysis software that runs on Windows. I have downloaded and used CLC Genomics Workbench, but only for two weeks. Any other software that I can use for longer...
12 December 2016 2,043 22 View
Hello, I am using QIIME to analyse my sequencing data. I have used it before with Illumina data with no problems, but now I have Illumina MiSeq data and four raw data files: two index files and...
12 December 2016 5,661 4 View
How I can clean & prepare Protein for MD simulations from the ligand-protein complex?
12 December 2016 7,059 3 View
Bioinformatics or Biostatistics
12 December 2016 3,327 5 View
12 December 2016 8,666 3 View
Answered
12 December 2016 256 4 View
12 December 2016 1,499 1 View
12 December 2016 6,642 5 View
I am working on a novel algorithm to calculate pairwise distance between nucleotide sequences and I am using those distances to construct phylogenetic trees. I need to test the accuracy of my work...
12 December 2016 6,994 3 View
12 December 2016 718 3 View
Hi all, I am new to the molecular dynamics simulation for biomolecules and wanted to asked some questions. Q1. what are some fundamental differences between AMBER, GROMACS, CHARMM and AMOEBA in...
12 December 2016 9,547 2 View
Here is an example. Lets say two SNPs are co-inherited 100% of the times, D' prime will always be 1, while r2 incorporates the information about allele frequencies and thus will be lower than 1 if...
12 December 2016 4,925 6 View
I'm try to use Qiime with RTAX assign_taxonomy method to deal with miseq PE data, which is not sequenced_through the V3 region. but the result turn out to nothing assigned! I follow the Qiime...
12 December 2016 5,101 5 View