Questions pertaining to organized collections of biological data.

learn more… | top users | synonyms

1
vote
1answer
37 views

Coordinates of amino acids in a protein sequence

In PDB format, the coordinates of each of the atoms are available. Are the coordinates for the amino acids available separately? As in say a protein sequence consisting of a chain of amino acids ...
1
vote
0answers
60 views

Reading BLOCKS database into Python or R [closed]

Are there any methods in programming languages that have been developed for reading the BLOCKS database? http://blocks.fhcrc.org/ What I want to do is read in the database file and compare sequences ...
1
vote
1answer
43 views

Data on Recombination rate and Gene Positions in Humans

I am looking for estimates of per base pair recombination rate in humans and indication on gene positions. The goal is to be a able to plot recombination rate in the y-axis and position (in bp) along ...
1
vote
0answers
36 views

How do I retrieve electronic annotation from Uniprot and GO records that relates to molecular function?

I'm interested in the endonuclease activity of the G3BP1 gene, specifically the uniprot record Q13283. An external link guides me to UniprotKB-KW electronic annotation. How can I retrieve valuable ...
4
votes
2answers
58 views

Grouping OMIM disease codes

I have ~100 sets of genes, and each set includes between 2 and 70 genes. I'd like to perform an enrichment analysis on each of these sets to test if they're enriched for OMIM disease labels. However, ...
2
votes
2answers
36 views

How to obtain a list of proteins sorted by the ~1400 unique protein folds?

The databases CATH and SCOP both have around 1400 unique protein folds recorded from analysis of the PDB. However, I do not see any method to access this particular data. A list of each of the 1400 ...
1
vote
0answers
30 views

how to visualise a network of proteins complex? [closed]

I would like to know how to visualise a complex of several proteins lets say I have a list of proteins ...
5
votes
1answer
102 views

How can I make a protein interaction/protein-complex network?

Let's say I have a list of proteins ID. I would like to know whether I can find any complex based on that list. Any example, explanation is appreciated. An example input is what you see below. What ...
3
votes
1answer
61 views

Understanding common identifier codes (IDs) in biology databases

I know this is very basic but I would like to understand it and it's difficult to know where to begin with a new database. I have the output: ...
2
votes
1answer
54 views

Protein-protein interactions search

I used STRING db in order to find all the interactions of the precursor protein APP. What I specifically need is a confirmation (supported by some article and experiments in it). But significant ...
4
votes
3answers
37 views

Identifiying a conserved residue in multiple PDB structures

I have a few hundred PDB structures of the same protein, and I need to identify a specific conserved residue in all of them. Originally I wanted to extract the sequences from the PDB files with ...
0
votes
1answer
18 views

what is the principle behind Allele Frequency Net Database

I just wanted to know what is the basic principle of Allele*Frequency Net Database. How are the frequencies present in them calculated??
0
votes
1answer
74 views

How can I find the most studied SNP of a gene?

How can I find the most studied SNP of a gene and diseases that the most studied SNP has been related to? I search in dbSNP database but I can't find it. What is the process?
1
vote
1answer
121 views

how to change format of ent file into PDB format?

whenever i download files from Protein Data Bank(PDB),they are downloaded in .ent format. How can i convert them into PDB format??
5
votes
3answers
124 views

Where can you find the quantities of each amino acid of a particular protein or food?

Taking a potato as an example. If I wanted to know how much µg or % of each of it's amino acids there are in 1 gram of pure potato protein, where can I find this information? Is there a freely ...
0
votes
1answer
34 views

Why does uniprot sometimes not label single-pass transmembrane proteins as “anchors”?

Currently, section 3a) of unitprot TRANSMEM reference page divides single-pass transmembrane proteins into 4 types: ...
1
vote
0answers
53 views

How to find name of the gene

Considering the kegg page, this page contains the description of the gene Edwardsiella tarda EIB202: ETAE_0074 . Now this gene has a name given in the page as : wabG. Now considering another gene 1 ...
9
votes
1answer
118 views

How can I find the mRNA sequence for a specific prokaryotic gene?

What I want to find out is the start of the transcription for a specific gene, how long the UTR is before the actual coding sequence starts. I've looked at various databases like NCBI Gene, Refseq or ...
1
vote
1answer
45 views

What does uniprot consider “unambiguous” evidence for the subcellular domain of a protein?

Uniprot has annotation for subcellular location of protein domains. This topological domain information of proteins is under the TOPO_DOM flag. In most cases the ...
4
votes
3answers
47 views

Is there a database providing information about optimum temperature and inactive temperature of enzymes?

I want to know optimum and inactive temperature of some enzyme, but I can't find these information in NCBI, wiki or UniProt. So I want to know if there are some database which provide these ...
5
votes
2answers
48 views

Is there a web tool for species identification?

I know this stack exchange provides the ability to post photographs of animals/plants for species identification, but is there a web resource that can automatically identify a plant/animal using image ...
0
votes
0answers
12 views

Do you know of any scratch assay video databases?

It would be of great help for a statistical work we have been asked to carry out at our University. Thank you very much in advance.
1
vote
0answers
31 views

Genotype-Phenotype databases?

Beyond the Stanford HIV database, what other databases out there provide a dataset linking virus/bacterial genotype to quantitative phenotype? I'm looking for high quality datasets to test machine ...
3
votes
2answers
142 views

Is there a database of cell images?

We're working on an algorithm for processing images of cells, similar to but much more basic than Cell Profiler, and we are looking for a large database of cell images to test our software. Can anyone ...
1
vote
1answer
61 views

open database of medical images

Does anyone know of an open repository of medical images (e.g., CT scans) organized by disease category? I'm working on some computer vision software that requires a large set of controls from which ...
0
votes
0answers
252 views

Online Database for PPG (Photoplethysmography) signals (both Infrared and Red light readings)

I am looking for an online Database for PPG (Photoplethysmography) signals for SPO2 (oximetry) analysis. I have tried several sources but they only have single datasets labelled "PLETH" and not ...
2
votes
1answer
36 views

Finding a reaction from a KEGG map

I have come across a map and a part of it looks like this: Now I have not been able to locate the reaction that converts alpha D-Glucose to Glucono-1,5-lactone but was successfully able to locate ...
8
votes
1answer
175 views

Database of Geographic Range of Species

Is there a database of organisms which would contain their queriable geographic location? I would need to perform a rather simple query, such as ...
13
votes
2answers
1k views

Why and how does uniprot list around 150,000 proteins in the human genome?

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns about 146,000 proteins. I was under the impression that there were only 20-25,000 protein ...
0
votes
1answer
31 views

Presence of reaction module in bacteria but not in Eukaryotas (human)

From the statistics page, I found that the Module-M00008 is present only in bacteria and not Eukaryotes. Why so? I noticed that all the compounds necessary or the reaction are present in human body ...
2
votes
1answer
37 views

Why is there a compound highlighted in red in a KEGG Module search?

Considering the following module: http://www.kegg.jp/kegg-bin/show_module?M00115+C00003 why is the compound C00003 marked in red?
1
vote
1answer
20 views

What information does the KEGG Module statistics page show?

While browsing through the home page of KEGG Module, I clicked the button named Module statistics. Can someone tell me what does these numbers signify? What are they the statistics of?
1
vote
2answers
95 views

Difference between modules in KEGG Module

The KEGG module M00115 includes a set of reactions while M00542 does not have any; it just shows the list of enzymes. Is the reaction set for M00542 still unknown?
5
votes
1answer
119 views

How to gather life-history traits data on bird species?

I am looking for a data base of life history traits for bird species. Is there such data base? If not, what are your advice on how to collect those data? Is there a handy website that list ...
2
votes
2answers
63 views

Database of medically validated SNPs

I'm looking for all possible sources of clinically tested human SNPs. There is a handful of databases that store SNPs (like dbSNP), but I only need those that have validated presence/absence of ...
6
votes
0answers
219 views

Is there a karyotype database for human cell lines?

I'm looking for the karyotype of a specific cell line. Some karyotype are well known, such as HeLa or some carcinomas, but some are very hard to find, such as LG2 (B cells). Is there a database ...
-3
votes
1answer
67 views

From where can I download the database created by Hsu et al for MORFs? [closed]

I am working on an independent research project for which I require access to the MORF database created by Hsu et al. From where can I download the database of MORFs of IDPs and their binding partners ...
5
votes
1answer
65 views

How to seek for available genetic data relevant to ecology and evolution?

I had a quick look online. There seems to exist many different website of database archiving. Some data might be free of charge while some others might not be. I found things such as Dryad, TreeBase, ...
1
vote
1answer
61 views

Human population growth - where can I find the data?

Out of curiosity, I'd like play around with data of human global demography. Where can I find data that describe the "per region (per continent for example) population size" versus time since the ...
0
votes
1answer
96 views

Finding Rna-Seq dataset for C. Elegans (Caenorhabditis elegans)

I want to find a RNA-Seq dataset for C. Elegans to use it in RNA-Skim software. For those who does not know RNA-Skim let me explain it a bit. It is a tool which is used to quantify RNA-Seq data using ...
3
votes
1answer
87 views

Resources of all known biochemical pathways?

I am looking for a encyclopedia or biochemical pathway atlas of all known or reported pathways. I am very much interested in network and systems biology. Also the references can be open databases, ...
3
votes
1answer
302 views

What is the difference between “physical interaction” and “genetic interaction”?

I searched sac1 in uniprot to know more about this gene. in interaction I selected this link and there I see that this gene has some "physical interactions" and "genetic interactions". I am wondering ...
0
votes
2answers
123 views

Difficulties understanding a pathway [closed]

I am not a biologist and I would love to understand what is going on with this pathway. I went to the description but it's still complicated, and I couldn't follow. Can someone please help me with it? ...
2
votes
0answers
118 views

Is there a database of known riboswitches?

I'm looking for sequences and annotations of known riboswitches, but so far I haven't found a resource that actually fulfills my requirements. The best database I found so far is Rfam, which has ...
5
votes
2answers
184 views

Where can I find mutation datasets for cancer?

My lab has been using TCGA data (somatic mutations and clinical data) to develop panels of genes and of mutations we expect to see in certain cancer populations. We'd like to validate our panels by ...
4
votes
1answer
185 views

What do “e” “-” “C” and “E” mean in this output?

I have given an input of this protein sequence: MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE from this website along ...
1
vote
0answers
36 views

Download FunCat Database for Programmatic Access

I am enriching RNA-seq data for the fungus Neurospora crassa and would like to be able to search the genome by functional category, determine similarity of genes by category membership, and any other ...
2
votes
2answers
103 views

Downloading specific yeast genes in an automated manner?

I have 6 genes of Candida albicans yeast namely orf19.723, orf19.5908, orf19.610, ...
3
votes
3answers
161 views

Where should I start looking for an online gene library?

Is there an online library that includes all known genes in stored in their nucleotide form of all living organisms? I'm presuming that such a database doesn't exist. So to kick of my search, how ...
0
votes
2answers
37 views

Resource for finding what proteins bind?

I have two lists of proteins (including phosphorylated forms). I want to determine which members of each list act on which members of the other list. What online resources exist for finding out what a ...