upload raw data to bionformatic tools

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Dante
Dante on 17 Nov 2022
Answered: Amith on 16 Sep 2024
Hi, I would like to import raw data to the bioinformatics tool (is it possible to use a ncbi database for identification)?

Answers (1)

Amith
Amith on 16 Sep 2024
Hi Dante,
You can import raw data into MATLAB for bioinformatics analysis and use the NCBI database for identification. Here’s a general approach to achieve this:
Importing Raw Data
  • Load Data: You can load raw data from various file formats such as FASTA, FASTQ, GenBank, and others using MATLAB’s Bioinformatics Toolbox.
data = fastaread('yourfile.fasta');
Using NCBI Database for Identification
  • Retrieve Sequence Information: You can retrieve sequence information from the NCBI database using the getgenbank function.
accessionNumber = 'NM_000520'; % Example accession number
data = getgenbank(accessionNumber);
  • BLAST Search: You can perform a BLAST search using the blastncbi function to identify sequences.
seq = 'ATGCGT...'; % Your sequence
[RID, RTOE] = blastncbi(seq, 'blastn');
  • View Results: You can use the Sequence Viewer app to explore nucleotide sequences.
seqviewer;
This workflow allows you to import raw data, retrieve additional information from the NCBI database, perform sequence identification, and visualize the results within MATLAB
Hope this helps!

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