CODEWITHSUNDEEP
sequencebioinformaticsbiopythonfasta
ryszard eggink
ryszard eggink

Reputation: 335

How do I determine the model organism from FASTA format

So I have this fasta format: For example 

>sp|A9X7L0|ANMT_RUTGR Anthranilate N-methyltransferase OS=Ruta graveolens OX=37565 PE=1 SV=1
MGSLSESHTQYKHGVEVEEDEEESYSRAMQLSMAIVLPMATQSAIQLGVFEIIAKAPGGR
LSASEIATILQAQNPKAPVMLDRMLRLLVSHRVLDCSVSGPAGERLYGLTSVSKYFVPDQ
DGASLGNFMALPLDKVFMESWMGVKGAVMEGGIPFNRVHGMHIFEYASSNSKFSDTYHRA
MFNHSTIALKRILEHYKGFENVTKLVDVGGGLGVTLSMIASKYPHIQAINFDLPHVVQDA
ASYPGVEHVGGNMFESVPEGDAILMKWILHCWDDEQCLRILKNCYKATPENGKVIVMNSV
VPETPEVSSSARETSLLDVLLMTRDGGGRERTQKEFTELAIGAGFKGINFACCVCNLHIM
EFFK

So I am wondering how do I determine if one is:

 Bacteria
 Viruses
 Archaea
 Eukaryota

Upvotes: 0

Views: 662

Answers (1)

BioGeek
BioGeek

Reputation: 22827

The anwser can be found when looking at the OS part of the header of your FASTA file. But suppose you don't have this information, then you would perform a BLAST search. If the letters in your sequence would consist of only A, T, C and G it would be a DNA sequence. But since they are not you are dealing with a protein sequence. So we need to use protein BLAST.

Copy/paste the FASTA file in the online tool:

BLAST search

Leave the rest at the default settings and click on the BLAST button. After some time you will get the following results:

BLAST results

You will see that there is a 100% similarity match found with Ruta graveolens (as mentioned in the FASTA header) and around 80% similarity match found in Citrus sinensis.

If you want to know to which domain these species belong, you can click on the link to the accession records. For Ruta graveolens that is A9X7L0.1. There you see that the common name of this plant is common rue which has the following taxonomy:

 Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
        Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;
        Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Rutoideae;
        Ruta.

Upvotes: 1

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