Questions tagged [identifiers]

Use this tag if your question is about translating some identifiers to others or about the rules of certain identifiers.

Filter by
Sorted by
Tagged with
0
votes
1answer
39 views

Mapping UniProt id to Entrez id

How can we get mapping from UniProt id to Entrez ID? I have UniProt id, but want to convert those ids to Entrez or Ensembl id.
1
vote
0answers
85 views

Is there a FASTA Sequence Description Nomenclature to Indicate a Split Sequence or Subsequence?

I have a nucleotide sequence where I am interested in aligning reads distinctly to one or another portion of the sequence. However, I would like to use a visualization tool such as IGV to view these ...
0
votes
0answers
28 views

Why the gene symbol aliases have significantly different sequences?

"Aliases" or "Synonyms" should represent the same gene but with different names. But when I try to find the sequence of one alias and try to match with another alias they are significantly different. ...
0
votes
1answer
16 views

how to get FlyBase ID conversion table

FlyBase uses systematic naming of genes, transcripts and proteins in a format FBtypeNUMBER. However, the numbers are not the same for genes and their products. For ...
2
votes
2answers
209 views

What do these files / annotations mean?

I have no experience in Bioinformatics and I need to understand what the annotations given here mean (I am including the first few lines, please see the link for more): ...
1
vote
1answer
198 views

Mapping RefSeq-ID or NCBI-ID (Entrez-ID) to EC number

I annotated my bacterial genomes using the new NCBI Prokaryotic Genome Annotation Pipeline and now, I want to annotate EC-numbers. In the master annotation file (.gff), I get the RefSeq-ID of every ...
4
votes
0answers
43 views

Gene not found in Affymetrix expression profiles

I am studying the ABA network in A. thaliana, consisting of HB7, ABI1 and AREB2. The AGI code I was given are, respectively: AT2G46680, AT4G26080 and AT1G45249. I downloaded the following file in ...
1
vote
1answer
31 views

Does read sequence identifier need to be unique for proper alignment?

I am preprocessing a set of scTHSSeq reads in which each read sequence identifier has been replaced with the cell barcode, e.g.: ...
0
votes
0answers
32 views

Why is Clostridium difficile toxin A + B outdated in snomed?

I'm looking at the new version of the Snomed dictionary and the concept 707993000 Clostridium difficile toxin A + B (substance) is deactivated (and outdated) since ...
1
vote
2answers
133 views

Obtaining identifier from plot of sequence GC%

I was looking at this script from https://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc297 and wanted to use it to determine outliers for tentative Horizontal gene transfer. The data set is ...
2
votes
0answers
25 views

Folded Protein Chunk Dimensional Classification?

Are there known scales and precisions required of dimensions for the classification of folded proteins given a starting chunk as defined by something like the clustering functionality of MSM Builder? ...
0
votes
0answers
425 views

Converting XLOC ids to UNIPROT ids

A friend of mine has sent me an Excel file with the results of the cuff-diff program that has the following header: ...
1
vote
1answer
124 views

What are the algorithms for biometric identification in large database?

I have been thinking about this problem and reading some related papers for sometime. The problem can be described as follows: Suppose that each biometric template is a $d-$dimensional vector. A ...
5
votes
3answers
438 views

How to determine the primary Uniprot accession number from a set of accession numbers?

Given a list of Uniprot IDs that are linked to an Ensembl gene ID, is there a way to systematically determine the UniProt accession corresponding to the protein product of the gene's primary ...
4
votes
1answer
383 views

Get canonical transcript from UCSC

I am using the following command to get all refseq genes from UCSC: ...
3
votes
1answer
128 views

What database do gene IDs starting with sp_v2 refer to?

I am a student trying to analyze GEO2r datas for one of my courses. The IDs given in the output are different for different series. I need to convert all of them to a similar format. In this process ...
5
votes
2answers
992 views

Fasta Sequence Identifier format?

I have been analyzing some virus DNA from the NCBI databases. The fasta sequences that I recieve from them have header lines that look like this: ...
4
votes
2answers
253 views

Convert Reactome Protein IDs to Pathway IDs?

I have a list of about 50k 'Protein IDs' from Reactome. Is there a simple way to get all the corresponding 'Pathway IDs' for each protein? What is the best service to use? (I'm guessing I can use the ...
11
votes
1answer
696 views

How to read and interpret a gene expression quantification file?

I have a gene expression quantification file from TCGA that contains the following lines: ...