<![CDATA[BOL: Annotating a sequence not yet published]]> https://bioinformaticsonline.com/answers/view/10479/annotating-a-sequence-not-yet-published? https://bioinformaticsonline.com/answers/view/10479/annotating-a-sequence-not-yet-published Wed, 07 May 2014 15:26:24 -0500 https://bioinformaticsonline.com/answers/view/10479/annotating-a-sequence-not-yet-published <![CDATA[Annotating a sequence not yet published]]> I have 198,991 bp long sequence. I ran it through Maker, Glimmer and GeneMarkS. All three gave me different number of predicted genes.Here I am talking about genes that I got through GeneMarkS.

Now when I am using BlastX to find the similar genes, I sometimes get highly dissimilar results. What does that indicate?

For eg:- for the given gene

>gene_id_13
ATGTTCGCGGGCGTAGTGCGCAGTTTCGTGCAGTGGAGACGAGTCGATGACACCGCCGTC
AGAGACGGTGAATGGCAAGACGAACGCGGCCGGATTGACTGGTTCGAATGA

After running blastX for gene 13, I get results with evalue 4.3 and above and sequences that are only 43% similar.

  33.1 33.1 81% 4.3 43% WP_017418739.1

>gene_id_14
ATGCTCGGACTGATGAAGGCCTGCAAAAAGCTCGGCCTGTCGTTCTGGCAGTATCTCTGT
GATCGCATCGGTGTCGATGGCCAGGCCATTCCGCCGCTGGCCGCCCTTGTCGGGGCAAAA
GCCTAA

with this gene, i got the following result

  76.6 76.6 97% 5e-16 80% CDM61676.1

Now if I combine genes 13 and 14. I got

  78.2 78.2 92% 4e-16 57% CDM61676.1

what does that suggest? 

Also, how to find the correct number of predicted genes when all three tools give different results?

Thanks

]]> ruchira