Questions tagged [sequence]
The sequence tag has no usage guidance.
13
questions
0
votes
0answers
20 views
Why is there a drop in the publication's rate of protein-sequences in UniProtKB/SwissProt
UniProt provides two databases 1:
UniProtKB/TrEMBL (TE) with entries for which the annotations are derived from the European Nucleotide Archive.
UniProtKB/SwissProt (SP) with entries for which the ...
0
votes
1answer
32 views
How do I generate sequence logo of ATGC against each position in R?
I am new in R sorry for the naive question. I want to generate the seqlogo for each position using R. Can anyone guide me? Thank you so much in advance.
...
1
vote
0answers
10 views
How to graph sequence ranges, for example intron sequences or conserved domains
I am a bioinformatics beginner.
I want to draw line graphs such that for a gene, say gene_A, intronic regions are (20,100), (500,600) and a conserved domain was found in (400-550), then I should get ...
1
vote
0answers
16 views
How to interpret complete genome sequence in NCBI
I have a very basic and quick question: does the complete sequence of nucleotides of an organism (for example this one that I am considering in my homework of Pyrococcus Fuoriosus) reported in NCBI ...
2
votes
1answer
39 views
How to know if ID correspond to nucleotide sequence or protein with a script
I have a text file that contains a list of IDs (314 sequences):
AVP78031.1
AVP78042.1
ATO98108.1
ATO98120.1
ATO98132.1
...
My goal is to make a script (maybe using ...
1
vote
0answers
20 views
How to use CD-HIT to filter protein sequences dataset by certain similarity threshold?
I am looking at using CD-HIT to efficiently filter my protein sequences dataset by a similarity threshold of 70% (cut-off). More precisely, what I want to achieve is that for all the remaining ...
0
votes
0answers
21 views
going from probe sequence to hgnc gene symbol
I have a bunch of (human) Agilent probes (both probe ID and the actual sequence, some custom array), and I would like to get the hgnc gene symbol based on the actual probe sequences, rather than the ...
3
votes
0answers
25 views
Template files for bioattributes and meta-data [closed]
I am in process of submiting my FASTQ files to the SRA database. I am a little confused about how to fill the biosample attributes and SRA metadata.
I would really appreciate if you anyone could share ...
-3
votes
2answers
56 views
get sequences begining with TA [closed]
I have a fasta file and the sequences in them are arranged like this:
...
0
votes
1answer
327 views
Remove Redundant Sequences from FASTA file in Python
I'm attempting to remove redundant sequences from a fasta file (from NCBI). When I execute this code, it returns the number of spots, not the number of sequences. (Number of spots: 408,293, Number of ...
5
votes
3answers
2k views
How to translate amino acid sequences to Nucleotide sequences
I want to convert a list of fasta ( protein sequences) in a .text file into corresponding nucleotide sequences. A Google search gives me result of DNA to protein conversion but not vice versa. Also, I ...
2
votes
1answer
87 views
Infer the new (Ban et. al) ribosomal nomenlature (ex. uL53 ) from the ribosomal protein's sequence
I'm trying to programmatically construct a name for each protein subchain in any ribosome from Uniprot in accordance with Ban et. al's 2014 proposal (excerpt given below) using PDB's and Uniprot's ...
2
votes
1answer
139 views
Appropriate tool or algorithm for sloppy alignment of degenerate bases
I have an optimization problem where I have a degenerate nucleotide sequence I want to align against subsets of a reference genome (exons, specifically, to make the problem more tractable).
The ...
