Questions tagged [sequence]

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Sequence Alignment for sequences with the same length

I am doing research on a new method of optimizing sequence alignment process (Needleman - Wunsch algorithm) but the idea would only work with sequences that have the same length. I am wondering if ...
MirzaK's user avatar
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2 votes
1 answer
41 views

Getting ALL Protein entries from Entrez for a particular taxonomic id

I'm trying to get ALL Proteins for a Taxonomic ID from Entrez using Esearch/Efetch and the following command: ...
The August's user avatar
2 votes
1 answer
147 views

1.What size PCR product will be generated using the primers (bold and underlined) in the sequence below?

I would like to know the steps of this question and how to determine the forward and the reverse primers and also the length of the sequence, without using NCBI. If you could explain and give an ...
Teo's user avatar
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3 votes
2 answers
88 views

Residue numbering in biopython

Is there an out-of-the-box function in the Bio.SeqIO module (in biopython) that can print a protein sequence (in command line) ...
Leptoceratops's user avatar
2 votes
2 answers
145 views

How do i search by these gene properties in NCBI's GenBank?

I want to search GenBank entries by gene product and taxon id. Taking the 16s rRNA as an example for a gene and Piscirickettsia salmonis (taxon:1238) for a taxon: https://www.ncbi.nlm.nih.gov/nuccore/...
Freezing Soul's user avatar
2 votes
1 answer
62 views

Sanger sequencing annotation error

I am a student in a Cancer lab. Working with sanger is new to me. While analyzing a report we found an insertion that has not been reported in any databases so far, we were working on checking if the ...
sana amir's user avatar
3 votes
1 answer
65 views

Downloading genes from NCBI in fasta format

I'm pretty new in bioinformatics. I need to download FASTA sequences of several genes. The list of genes I have assembled consists of 140 genes, so I'd rather do this through via code than download ...
Vjon's user avatar
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1 vote
1 answer
155 views

finding matching motifs in a sequence and their position

I am trying to find some matching motifs on a sequence, as well as the position that the motif is located in and then output that into a fasta file. The code below shows that the motif ...
thole's user avatar
  • 143
2 votes
0 answers
47 views

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 ...
snap_v's user avatar
  • 21
1 vote
3 answers
944 views

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 ...
Marco's user avatar
  • 161
1 vote
1 answer
39 views

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... ...
Parasu Nagesh Sunag's user avatar
3 votes
1 answer
165 views

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 ...
kormi's user avatar
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2 votes
1 answer
86 views

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/ ...
KaPy3141's user avatar
  • 151
0 votes
1 answer
55 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. ...
ray's user avatar
  • 11
1 vote
0 answers
12 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 ...
user12409's user avatar
1 vote
0 answers
22 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 ...
HelpNeederStudent's user avatar
2 votes
1 answer
72 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 ...
Mauri1313's user avatar
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1 vote
0 answers
72 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 ...
Frix's user avatar
  • 11
3 votes
0 answers
32 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 ...
Riya's user avatar
  • 307
-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: ...
Amit's user avatar
  • 133
2 votes
1 answer
763 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 ...
User's user avatar
  • 53
5 votes
3 answers
4k 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 ...
user3289492's user avatar
2 votes
1 answer
92 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 ...
rtviii's user avatar
  • 342
2 votes
1 answer
277 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 ...
Alex Reynolds's user avatar