upload raw data to bionformatic tools

Hi, I would like to import raw data to the bioinformatics tool (is it possible to use a ncbi database for identification)?

Answer 1

[Amith]

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!