9
votes
Accepted
How to read and interpret a gene expression quantification file?
The first column contains Ensembl gene identifiers, and the suffix is a version number that can be used to track changes to the gene annotations over time. From the Ensembl Stable IDs documentation:
...
- 5,110
6
votes
How to get strain names/ids contained in a multi FASTA file using seqkit?
The nice thing about seqkit is that the answer is really simple and memorable:
seqkit seq -n sequences.fasta
This will output a ...
- 409
6
votes
Accepted
Convert Reactome Protein IDs to Pathway IDs?
If you don't mind hitting it 50k times and are OK with python3...
...
- 19.8k
5
votes
Accepted
What do these files / annotations mean?
You are looking at the supplementary data of a paper. That seems to have given you a list of features, and some information about those features. Specifically, you seem to have a list of two types of ...
- 10.6k
5
votes
Accepted
Fasta Sequence Identifier format?
The gi is an abbreviation for "Genbank identifier".
This is a pretty standard convention used by data stored in NCBI databases. There used to be a pretty ...
- 5,110
5
votes
Accepted
What database do gene IDs starting with sp_v2 refer to?
This is possibly a wild goose chase, but a lot of searching led me to this sample:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2536852
Which appears to exhibit accessions of the right ...
- 861
5
votes
Why the gene symbol aliases have significantly different sequences?
At Ensembl, we categorise synonyms as anything that a gene might also be known as. This includes older names for them, since those names will be in the literature, including where a gene has been ...
- 1,779
4
votes
How to get strain names/ids contained in a multi FASTA file using seqkit?
You can trivially do this with standard *nix tools. Here are a few options:
...
- 10.6k
4
votes
Accepted
How to determine the primary Uniprot accession number from a set of accession numbers?
Reposting my answer from the related ticket in the Biology section:
I think there is an issue with the terminology. The "primary" accession number, is the first accession number in cases where an ...
3
votes
Convert Reactome Protein IDs to Pathway IDs?
On Reactome website they have at the download page mapping files (uniprot, ensembl, etc.), but unfortunately not for the protein IDs you are using (stable identifiers).
I had contact with their ...
- 3,601
3
votes
How to determine the primary Uniprot accession number from a set of accession numbers?
Consider the circumstances in which entries will have more than one accession (taken from the same page you linked in the original post).
Entries will have more than one accession number if they have ...
- 5,110
3
votes
Accepted
Get canonical transcript from UCSC
You can link them with the kgXref table, since kgXref.refseq == refGene.name and ...
- 19.8k
3
votes
Accepted
Folded Protein Chunk Dimensional Classification?
CATH
The CATH database classifies protein by fold: https://www.cathdb.info/
So the value from that is probably the most useful for you.
Crystallographic conditions
pH
Salinity
Dissolved Sugars
...
- 4,274
2
votes
Accepted
Does read sequence identifier need to be unique for proper alignment?
What tool did you use to replace the read names? Can you modify that to split up the reads into separate files or encode the cell barcode in the read description instead of the read name?
Typically ...
- 2,584
2
votes
Obtaining identifier from plot of sequence GC%
There are various attempts to guess putative horizontal gene transfer using sequence composition (kmer-frequencies or GC content), you do not have to implement a new method by your own.
I co-...
- 5,652
2
votes
Accepted
Obtaining identifier from plot of sequence GC%
The tricky bit here is that you need a list of sequence records sorted in the same order as the CG values. You can accomplish this by making tuples of the seq records and GC values, then sorting the ...
- 1,816
2
votes
What are the algorithms for biometric identification in large database?
I think that a very nice example of what you are talking about saying the word bigger, is probably a microarray transciptional analysis of RNA extracted from a biological sample. Simplifying, in these ...
- 21
2
votes
Mapping RefSeq-ID or NCBI-ID (Entrez-ID) to EC number
You can use Entrez Direct for this as follows:
efetch -db protein -id YP_805528.1 -format gpc -mode xml | xtract -insd Protein EC_number
YP_805528.1 6.3.2.13
- 1,286
2
votes
Accepted
What type of Protein ID is this?
I'm not sure I understand the question, but XP_019970915.1 is an 'NCBI Reference Sequence' ID for 'erythrocyte binding antigen-181' (https://www.ncbi.nlm.nih.gov/protein/XP_019970915.1/). If you look ...
- 707
2
votes
Mapping UniProt id to Entrez id
The Retrieve/ID mapping tool from Uniprot allows you to convert from Uniprot to entrez ID and vice-versa. It is available here. Just select the appropriate values in the ...
2
votes
Why the gene symbol aliases have significantly different sequences?
Answer from @devon-ryan, converted from comment:
Both, that's why NAT5 is no longer a human gene symbol.
NAT5 does not equal NAA20, it's an out-dated name for it. Names change over time as people ...
2
votes
Accepted
Convert Entrez gene ids and HUGO symbols, whose genome assembly is unknown, to GRCh38 Ensembl gene ids
Hugo names don't really have an associated assembly. They are just the official name of the gene in human. You will find them in all assemblies (except if they hadn't been annotated/identified in one ...
- 10.6k
2
votes
BAM files with no RNAME and POS, how to map contents to SNPs?
These lines (with no REF or POS) are unmapped reads. If those lines are the entirety of the BAM file, then it is simply another file format to store the raw sequenced reads (as an alternative to FASTQ ...
- 15.1k
2
votes
Accepted
VEP annotation INFO field Ensembl IDs and locations
You need to set your expectations clearly instead of just saying "Does not agree". I'm taking a guess here - your statement is that the 2/4 of the gene co-ordinates do not overlap the ...
- 2,498
1
vote
Remove variable sequence component within a tree text file
Lots of ways to do this, but here's one way using sed:
sed 's/TRINITY_\([^_]\+\)_\([^_]\+\)_[^:]\+/\1_\2/g' file.tree
The above applies a substitution to capture ...
- 3,287
1
vote
What is the best way to programmatically convert Ensembl ids from one release to other? e.g. transcript ids from release 75 to 100
The ID history converter is available as a Perl script.
This script accesses these MySQL tables, so you could query these tables directly.
Note that the mapping session is only one release at a time, ...
- 1,779
1
vote
How to replace sequence identifiers in a fasta with OTU IDs from another file?
You can put you fasta file in a single line per sequence:
perl -pe 'if(/\>/){s/\n/\t/; s/>//; s/\n//}' file.fasta > file.tsv
This line will create the ...
- 769
1
vote
How to replace sequence identifiers in a fasta with OTU IDs from another file?
You can do it with bash quiet easy. First create a backup of your fasta file with
cp otu.fasta otu_backup.fasta
Then you can run:
...
- 629
1
vote
Accepted
how to get FlyBase ID conversion table
Indeed the web interface does not seem to link the full translation table, but it is available on their ftp server at ...
- 5,652
1
vote
What do these files / annotations mean?
gi looks like a Genbank Identifier. You can search for the 10 digit number following gi| at the Genbank website.
- 1,012
Only top scored, non community-wiki answers of a minimum length are eligible