Bioinformatics is a broad field that interfaces a variety of life science disciplines with a variety of quantitative sciences. Questions on Bioinformatics are expected to have a direct biological component to them or they may belong on Stackoverflow or Superuser.
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1answer
71 views
Problems with analysis of small RNAseq data - Adapter trimming
I have always faced a problem while analyzing small RNAseq data, at the step of adapter trimming.
Overview of small RNAseq (Illumina)
RNA is size fractionated using columns or PAGE
3' and 5' ...
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1answer
55 views
What is the best way to read and normalize large amounts of Agilent data into R? [closed]
I have a large amount of Agilent data (580 text files that are ~200 MB in size each) that I'd like to normalize. I've run into a problem in that my machine (with 8 GB of memory) still runs out of ...
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1answer
28 views
Where can I find a transcriptome of a normal uveal melanocyte?
I am looking for a database where I could find a transcriptome (say obtained with a microarray analysis) of one (or ideally many) normal uveal melanocytes ?
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1answer
51 views
TFBS predictions for yeast and pombe?
Are there any resources out there for TFBS (transcription factor binding site) predictions for the yeast (S. cerevisiae) and S. pombe genomes? Even if these are only de novo predictions, I would like ...
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0answers
29 views
How can I view modENCODE data faster?
I am trying to view several data tracks in the modENCODE GBrowse genomic browser. However, the site is so slow, it is practically unworkable. Is there a faster way to explore the data?
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0answers
48 views
SAM and Reverse Complements [closed]
Assume a read aligner (such as e.g. BWA) is fed with a pattern P = GACT. Now, the text that ...
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2answers
49 views
Deterministic model of lambda-phage lysis/lysogeny [MATLAB]
Project 1 Base:
Can someone please help me understand what I need from Project 1 Base code to do questions 1 and 2 from the first image? I'm new to MATLAB so a thorough explanation would be ...
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1answer
27 views
SNPs mapping into protein
Starting a new project on protein-protein interactions and SNP analysis tool development. I would like to ask how does SNPs is mapped into protein? What does mapping means?
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1answer
31 views
TCGA data, and bioinformatics design questions for SNP/ mirna analysis
It's my first time posting to this forum but was looking for some help on the data aspects of this project.
My tools of choice would be in python/R .
Goal: I'm looking to create a disease specific ...
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0answers
25 views
Modeller - Convert FASTA to PIR
I am doing a basic modelling following the instructions here. But different target / template sequences.
http://salilab.org/modeller/tutorial/basic.html
Do I need to convert the FASTA to PIR with a ...
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0answers
34 views
Confusion related to the use of PCA to determine the background network
I was reading this paper related to use of gene expressions for predicting the drug response. I have this confusion, the paper has used PCA on the covariance matrix formed by the genes to get what is ...
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35 views
Choosing biology course for minor in computation biology [closed]
I apologize if this question is not right for this forum. I will be transferring to UC Davis where I will be majoring in computer science. I'm considering specializing in scientific computation and ...
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26 views
Recombination-based vs. Sequence-based genetic mapping
Now that sequencing is becoming increasingly cheap, what is the value of recombination-based genetic mapping against the sequence-based genetic mapping?
I think that in the past recombination-based ...
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2answers
84 views
Specific enzyme for C. elegans [closed]
We are looking for an enzyme that appears in C. elegans but isn't common for: human, Drosophila or mouse.
We need it for a little research project, thanks for your help!
