Questions tagged [sequence]

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Is there a way antiSMASH can be used to screen a large number of genomes just for one type of biosynthetic gene cluster?

When we use antismash command with the genome sequence file as follows: antismash GCA_002095535.1_ASM209553v1_genomic.gbff it screens the genome for all the ...
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1 vote
3 answers
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How can I remove FASTA sequences with an asterisk inside the sequence?

I have several protein sequences with an asterisk in the middle of the sequence, and I'd like to remove those sequences. In the example below, I have three sequences: From this example, I would like ...
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1 answer
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Problem with sequence alignment

I'm trying to find if the peptides in column A are present within the longer peptides of column B. Pairwise alignment tools take the data from both columns as one string (i.e., TIIDYTNNHYTNNHLEII... ...
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1 vote
0 answers
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Identification of unique chains in proteins by sequence similarity

I'm trying to find unique chains or proteins within their PDB files. Many proteins have multiple chains, but very often they are identical (say, the PDB file consists of 4 homodimers, for example, so ...
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2 votes
1 answer
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How to get coding sequences (CDS) of UniProt reference proteomes?

I downloaded the following reference proteomes: https://ftp.ebi.ac.uk/pub/databases/reference_proteomes/QfO/ ...
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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 ...
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1 answer
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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. ...
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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 ...
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1 vote
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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 ...
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2 votes
1 answer
43 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 ...
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0 answers
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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 ...
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3 votes
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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 ...
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  • 131
-2 votes
2 answers
57 views

get sequences begining with TA [closed]

I have a fasta file and the sequences in them are arranged like this: ...
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2 votes
1 answer
467 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 ...
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  • 53
5 votes
3 answers
3k 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 ...
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2 votes
1 answer
89 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 ...
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  • 270
2 votes
1 answer
171 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 ...
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