Questions tagged [sequence]

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30 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
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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
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0answers
14 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
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1answer
38 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
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0answers
18 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
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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
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0answers
24 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
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2answers
55 views

get sequences begining with TA [closed]

I have a fasta file and the sequences in them are arranged like this: ...
0
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1answer
220 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
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3answers
1k 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
86 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
115 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 ...