HOW TO START

STEP 1 - Define your work order

Here, we are suggesting the work order and in silico analysis programs based on the biological sequence obtained from the database into a Flowchart.

STEP 2 - Sequences in bioinformatics

Once you have defined your job, you need to know that in bioinformatics some programs require a sequence of nucleotides to analyze your information. These sequences are listed below. 

FASTA format 

To use most programs here, you may need to submit a FASTA sequence. This is a format of one line before the nucleotide sequence, which must begin with (">"), followed by a unique SeqID (sequence identifier).

All information must be on a single line of text. Limit the SeqID to 25 characters or less. The SeqID can only contain letters, digits, hyphens (-), underscores (_), periods (.), colons (:), asterisks (*) and numbers signs (#).

The line following the FASTA definition line begins the nucleotide sequence. It is recommended that each line of the sequence is no longer than 80 characters.

Examples of correctly formatted FASTA definition lines for nucleotide sequences from NCBI:

• >Seq1 [organism=Streptomyces lavendulae] [strain=456A] Streptomyces lavendulae strain 456A mitomycin radical oxidase (mcrA) gene, complete cds.

• >ABCD [organism=Plasmodium falciparum] [isolate=ABCD] Plasmodium falciparum isolate ABCD merozoite surface protein 2 (msp2) gene, partial cds.

• >DNA.new [organism=Homo sapiens] [chromosome=17] [map=17q21] [moltype=mRNA] Homo sapiens breast and ovarian cancer susceptibility protein (BRCA1) mRNA, complete cds.
  
  

BARE sequence

This term refers to a sequence of nucleotides or amino acids in its "raw" format. It is a pure sequence of just a string of A, T, C, G or amino acids represented by letters. It does not include additional annotations such as gene names, descriptions, locations in the genome.

This is often used in the initial stages of analysis, sequencing studies and data sharing with systems or researchers.

Examples of bare sequences

• DNA sequence: ATGCTGGCATG

• Protein sequence: MSLLFISALYWV

PDB file

Some bioinformatics programs require a PDB file as input. This file stores the three-dimensional information of molecules. Generally readable as text, a PDB file contains the coordinates of each atom in the molecule, describing their arrangement in three-dimensional space, including important information such as chemical bonds, polypeptide chains, chemical groups, among others.

PDB files can be obtained from databases and modeling tools.

This type of file is mainly used for structural model validation, molecular docking, and three-dimensional visualization through programs like PyMOL or Chimera.