Questions pertaining to organized collections of biological data.

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14
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3answers
153 views

Where can I find historical data on world-wide ecology parameters?

I hope this is the right StackExchange forum for such a question. I'm looking for large data sets on world-wide ecology parameters, such as annual temperatures by latitude, annual rainfall, CO₂ and O₂...
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 ...
13
votes
2answers
204 views

Can two protein secondary structures “overlap” in the PDB?

I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file: ...
9
votes
1answer
127 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 ...
8
votes
1answer
182 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 ...
7
votes
1answer
67 views

How to search for organisms by criteria such as growth substrate and overflow metabolites?

I'm looking for a database or a systematic way to search for organisms which meet certain criteria. My criteria descending importance are: growth substrate chemolithoautotrophy (on which substrate) ...
6
votes
1answer
112 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 ...
6
votes
3answers
111 views

What is a good source that will help me classify protists?

I am a 15 year old that enjoys looking at the micro world. The only issue that I have is that I can't find a good online source that will help me classify the name of the micro organism that I'm ...
6
votes
0answers
235 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 ...
5
votes
3answers
141 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 ...
5
votes
2answers
193 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 ...
5
votes
1answer
73 views

Calling for Free Online Data for Paediatric ECG?

I need free online data about heart murmurs to study these: heart murmur frequency , S2 heart sound frequency and its split, murmur timing, and duration, murmur intensity, S3 sound presence and ...
5
votes
2answers
50 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 ...
5
votes
1answer
132 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 ...
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, ...
5
votes
2answers
718 views

Are there any open plant databases (database/library/collection), containing species information and pictures?

I would like to download a plant database containing photos and species details. Do you know if there are any openly available online?
4
votes
1answer
190 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 ...
4
votes
2answers
62 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, ...
4
votes
3answers
40 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 ...
4
votes
3answers
49 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 ...
4
votes
1answer
322 views

Local storage of NCBI database in MongoDB [closed]

My short term goal in a project is to build a local database of the NCBI dbSNP database. The data and schema are available on the FTP site(). I was going to implement the database using MySQL, but I ...
4
votes
1answer
150 views

Antibody-antigen database

Is there a database where I can find an affinity estimate if I provide a given antibody and a given antigen sequence ? Input : antibody + antigen sequence Output : quantitative binding/affinity ...
4
votes
2answers
175 views

Database of Multicellular and Unicellular organisms?

I'm trying to annotate a list of organisms taken from NCBI for cellularity (unicellular or multicellular). Does any of you ever found a database with association between an organisms' name or taxa and ...
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 ...
3
votes
1answer
88 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
2answers
151 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 ...
3
votes
1answer
127 views

Do there exist publicly available Genome sequences of a family?

I would like to explore the genome sequence of a publicly available genome sequences of a family (like mother, father, son, daughter...). If such human genome sequences are not publicly available at ...
3
votes
1answer
63 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: ...
3
votes
1answer
332 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 ...
3
votes
1answer
53 views

Is there any database with RNA classification?

I am looking for a database that would provide classification of various types of RNA - information about its structure, function, etc.
3
votes
2answers
35 views

How to find PDB id of an amino acid sequence

Suppose I have an amino acid sequence whose PDB id is unknown. Is there in online server that can find the PDB id of the corresponding amino acid sequence? is there any site that will find the pdb ...
3
votes
1answer
102 views

What is a good source for info on disease frequency distribution among age groups?

I need information on the disease frequency distribution among age groups for an Android app I'm building... Hopefully I've come to the right place. Is there a good data source for this? Like a ...
3
votes
2answers
44 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 ...
3
votes
0answers
54 views

Database of Medical Assertions

Can anyone point me toward a computationally-accessible database of medical assertions? I'm looking for something where each row in the database contains a single unit of knowledge. It could either be ...
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?
2
votes
2answers
105 views

Downloading specific yeast genes in an automated manner?

I have 6 genes of Candida albicans yeast namely orf19.723, orf19.5908, orf19.610, ...
2
votes
1answer
379 views

What does chromosome CHR_Un, CHR_MT in the ftp site of NCBI mean?

I am not a biologist. But need some genetic data. So I searched internet and reached NCBI's website. I came to know from the FAQ page that I can the complete genome data of organisms from ftp://ftp....
2
votes
1answer
37 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 ...
2
votes
2answers
65 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 ...
2
votes
1answer
101 views

Where to obtain metabolic pathway datasets

I've been looking through the files available at www.reactome.org along with some others but I only find images/pdfs of metabolic pathway diagrams. Where is the actual data these pathways are drawn ...
2
votes
2answers
631 views

What's a good and reliable database on the pharmacodynamic and pharmacokinetic data of drugs both approved and unapproved?

What's a good and reliable database for the pharmacodynamic and pharmacokinetic data of drugs both approved (in the US and elsewhere) and unapproved?
2
votes
1answer
104 views

How to retrieve logical expression (KO based) for reactions from KEGG?

Whether a module is complete or not can easily be checked by evaluating the Definition entry associated with the module; e.g. in module M00010, it is given by <...
2
votes
1answer
83 views

What type of distribution should binding affinities fit?

I've been averaging Ki values from the PDSP Ki Database, and I can't help but to wonder: how I can determine p values for the binding affinities, so I can exclude anomalies in the data if need be?
2
votes
0answers
124 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 ...
2
votes
0answers
72 views

dbSNP database table desciptions

I am trying to build a local implementation of dbSNP. I would like to know the descriptions of tables listed on ftp://ftp.ncbi.nlm.nih.gov/snp/database/organism_data/human_9606 and on ftp://ftp.ncbi....
2
votes
0answers
31 views

Is there a database of pollen-seed distances across plant species?

I was enjoying Richard Smith's excellent answer to this question, and wondered: If you consider the pollen/seed distribution range to be plant locomotion, is there a database that compares these ...
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 ...
1
vote
1answer
57 views

How to batch convert gene names to protein IDs in Uniprot?

I have a list of >1000 "ordered locus names" from the STRING database (also called gene numbers, ORF numbers, or CDS numbers by uniprot). They're in the form of 'b0014', 'b0015', etc. I'd like to ...
1
vote
1answer
33 views

Distribution of Exon and Intron Sizes

Goal I am trying to get a distribution of Exons and intron sizes in Three-Spined Stickleback (Gasterosteus aculeatus). Data downloaded I downloaded some data from Ensembl. More precisely, I went ...
1
vote
1answer
50 views

Coordinates of amino acids in a protein sequence [closed]

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 MKL......