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.
2
votes
3answers
84 views
What percentage of protein isoforms have different functions?
I am looking for studies on how many protein isoforms have different functions, preferably in human. We know that a great many, if not most, of human genes are alternatively spliced and that many ...
1
vote
1answer
26 views
Mapping a mutation to known SNP, 3' UTR, miR
I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information.
The ssm is in the following format:
...
0
votes
1answer
54 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 ...
6
votes
0answers
39 views
Using the IMGT/GENE-DB service to find RSS
I'm trying to get the data for the Human and Mouse 12 and 23 Recomination
Signal Sequences (RSS), to run a classification algorithm on it. I'm not a
biologist, so I apologise in advance for my ...
4
votes
0answers
78 views
Is there a comprehensive database of fossils (with images) online?
Not sure if this is the best stackexchange to ask...
I have not been able to find a decent database of fossils on the web, does one exist?
Here are some of the links I have found through Wikipedia ...
2
votes
0answers
63 views
Software for counting fly eggs
Is there any software that could be used to rapidly (quicker than humans) count the eggs laid by Drosophila on a substrate by placing them under a microscope with a camera attached? The eggs are laid ...
2
votes
0answers
27 views
What does conditional analysis of a SNP in a GWA study entail?
I am familiar with the use of tag-SNPs in genome-wide association studies to identify gene loci involved in complex traits, but I keep seeing the term "conditional analysis" used without any ...
2
votes
0answers
111 views
Too few transcripts from transcriptome assembler Oases
I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks.
Here is my running command:
...
1
vote
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?
0
votes
0answers
17 views
best known indexing method / transformation to coordinates for gene sequences
What would be the best known method to transform a gene or proteine sequence to some coordinate space (so $t(G)$ is the transformed sequence) complying to following rules:
similar sequences ...
0
votes
0answers
25 views
Reverse complement of reconstruction model for assembling reads
One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this ...
0
votes
0answers
30 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 ...
0
votes
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 ...
0
votes
0answers
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 ...
