Overview

Our system allow user to upload files containing processed nucleotide sequences and identify what species each file contains with the below nucleobases.

Supported nucleobases

The system supports a combination of nucleobase symbols used in DNA sequencing. Each letter stands for a specific nucleobase or a group of nucleobases:

  • Name
    A
    Type
    Adenine
    Description

    A purine nucleobase that pairs with Thymine in DNA through two hydrogen bonds.

  • Name
    G
    Type
    Guanine
    Description

    Another purine nucleobase, which pairs with Cytosine in DNA via three hydrogen bonds.

  • Name
    C
    Type
    Cytosine
    Description

    A pyrimidine nucleobase that pairs with Guanine.

  • Name
    T
    Type
    Thymine
    Description

    Also a pyrimidine nucleobase, pairing with Adenine.

  • Name
    N
    Type
    Any (∀)
    Description

    Any Nucleotide (A, G, C, or T).

  • Name
    M
    Type
    Amino group
    Description

    Amino group, representing either A or C.

  • Name
    R
    Type
    Purine
    Description

    Purine, representing either A or G.

  • Name
    W
    Type
    Weak (A or T)
    Description

    Weak, representing either A or T.

  • Name
    S
    Type
    Strong (G or C)
    Description

    Strong, representing either G or C.

  • Name
    Y
    Type
    Pyrimidine
    Description

    Pyrimidine, representing either C or T.

  • Name
    K
    Type
    Keto
    Description

    Keto, representing either G or T.

  • Name
    V
    Type
    Not T
    Description

    Not T (A, C, or G).

  • Name
    H
    Type
    Not G
    Description

    Not G (A, C, or T).

  • Name
    D
    Type
    Not C
    Description

    Not C (A, G, or T).

  • Name
    B
    Type
    Not A
    Description

    Not A (C, G, or T).

Preparing your data

Data can be prepared using various formats, such as FASTA, CSV, TXT, remember to remove raw reads.

Example.fastalimit: 5MB

Using FASTA file

The FASTA format is a text-based format for representing nucleotide sequences (like DNA or RNA) or peptide sequences (amino acids), commonly used in bioinformatics. It is a simple and widely adopted format for input into many sequence analysis tools and databases, there are two main parts:

  1. Header Line: Begins with ">" and includes the sequence name or identifier.
  2. Sequence Lines: Contain the genetic sequence in letters (like A, G, C, T for DNA, or amino acid codes for proteins).

Example.fasta

>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) OX=654924 GN=FV3-001R PE=4 SV=1
VRVTVVADBKMWTDKRDSCCBBVKHRDDWNTGKGMNADCDBSCGABBVTRWMMMVTKBGM
HYSHYGSGMKNGDYCVDMGKKCAYBTARBRHBDWVAWVNHNWMWNMTGWGRCCYCRYDMD
STKRGSVVTVTDVRCTSYMHRKTVBDCTRNDCVNSSBMGDTSWNTSKYRABGWVWSYABY
WHGCHCTRHWKWSVVCCAD
>sp|Q6GZX3|002L_FRG3G Uncharacterized protein 002L OS=Frog virus 3 (isolate Goorha) OX=654924 GN=FV3-002L PE=4 SV=1
VRVTVVADBKMWTDKRDSCCBBVKHRDDWNTGKGMNADCDBSCGABBVTRWMMMVTKBGM
HYSHYGSGMKNGDYCVDMGKKCAYBTARBRHBDWVAWVNHNWMWNMTGWGRCCYCRYDMD
STKRGSVVTVTDVRCTSYMHRKTVBDCTRNDCVNSSBMGDTSWNTSKYRABGWVWSYABY
WHGCHCTRHWKWSVVCCAD
... ...

 

Example.csvlimit: 5MB

Using CSV file

The CSV (Comma-Separated Values) format is a simple text format used to store tabular data (like a spreadsheet or a database) in plain text. Each data separated by comma will be a single genetic reads.

  1. No Header: Do not include any header, just include reads separted by comma.

Example.csv

VRVTVVADBKMWTDKRDSCCBBVKHRDDWNTGKGMNADCDBSCGABBVTRWMMMVTKBGM
HYSHYGSGMKNGDYCVDMGKKCA,YBTARBRHBDWVAWVNHNWMWNMTGWGRCCYCRYDM
STKRGSVVTVTDVRCTSYMHRKTVBDCTRNDCVNSSBMGDTSWNTSKYRABGWVWSYABY
WHGCHCTRHWKWSVVCCAD,VRVTVVADBKMWTDKRDSCCBBVKHRDDWNTGKGMNADCD
HYSHYGSGMKNGDYCVDMGK,KCAYBTARBRHBDWVAWVNHNWMWNMTGWGRCCYCRYDM
STKRGSVVTVTDVRCTSYMHRKTVBDCTRNDCVNSSBMGDTSWNTSKYRABGWVWSYABY
WHGCHCTRHWKWSVVCCAD
... ...

 

Example.txtlimit: 5MB

Using TXT file

The TXT format is a plain text format, you can separate your data with either comma or new line.

  1. Use comma: Do not include any header, follow CSV style
  2. Use newline: Make sure each reads are separated with a new line.

Example.txt

VRVTVVADBKMWTDKRDSCCBBVKHRDDWNTGKGMNADCDBSCGABBVTRWMMMVTKBGM
HYSHYGSGMKNGDYCVDMGKKCAYBTARBRHBDWVAWVNHNWMWNMTGWGRCCYCRYDMD
STKRGSVVTVTDVRCTSYMHRKTVBDCTRNDCVNSSBMGDTSWNTSKYRABGWVWSYABY
WHGCHCTRHWKWSVVCCAD
VRVTVVADBKMWTDKRDSCCBBVKHRDDWNTGKGMNADCDBSCGABBVTRWMMMVTKBGM
HYSHYGSGMKNGDYCVDMGKKCAYBTARBRHBDWVAWVNHNWMWNMTGWGRCCYCRYDMD
STKRGSVVTVTDVRCTSYMHRKTVBDCTRNDCVNSSBMGDTSWNTSKYRABGWVWSYABY
WHGCHCTRHWKWSVVCCAD
... ...

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