Details About Indel Experimentation Result


[Q: Query]


  • Programs used in this experiment: Artemis1, BLAST2
  • Source dir. for all fasta/ Overview directory.
  • All Clustered fasta show quite the same INDEL pattern.
    That’s why they are kept in same directories. (i.e. Q-56(042 + 053 + 038))




INDEL Insights

Select Tab. Then, Click ▶ button for details

Significatnt INDEL Category:

Q-56093:




INDEL Details



Nucleocapsid(N gene) mobile element to –> ORF8
INDEL = 1* (Type: Insertion) 

  Mobile Element Insertion = (27910-27985)
    tccaccaaacgtaatgcggggtgcatttcgctgattttggggtccattatcagacatttt
    agtttgttcgtttaga

Comparative Genomics



Q-56049 + Q-56048 + Q-56100 + Q-56358:




All these queries share exact same deletion profile.
INDEL = 1 (orf8) Deletion 

 ORF8 Length = 27894................................28257
   
   Deleted     = _____________(27913-28254)_______________

Comparative Genomics





Q-56042 + Q-56053 + Q-56038:




All these queries share same deletion profile.
INDEL = 1 (orf7a) Deletion
(Sequence Homology Threshold was set: 90)

 ORF7a Length = 27394..............................27759
   Deleted      = _____________~(27476-27668)_____________

~ = Approximately around. <10 bases up/down. Apprx. pos. at start. All end at 27668.

Comparative Genomics




Less Significant INDEL Category:

Q-56289 vs rf vs Q-56316:




INDEL = 2 

 *1. (Q-56289 vs rf) Blue Region = Inverted Genetic Element
       (1-53)
       gatctacaagagatcgaaagttggttggtttgttacctgggaaggtataaacc

    2. Q-56316 vs rf
       Ambiguous\ N = (49-586) nucleotide

Comparative Genomics




Q-56201:




INDEL = 1

  agatctgttctctaaacgaac (1-21) +
    Ambiguous\ N = (22- 268) nucleotide

Comparative Genomics




Q-56198:




INDEL = 4 (Orf1ab:1-3; S:1)


(Sequence Homology Threshold was set: 50)

  1. (76-590)
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnng
       ctcgtacgtggnnnnnnnnnnnnnnnnnnngaggtcttatcannnnnnnnnnnnnnnnnn
       nnnnnnnnnncttgtggcttagtagaagttgaaaaaggcnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnagcagaactcgaaggcattcagtacggtcgtagtggtgagacacttggnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
    2. (8628-8860)
       cnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnh
    3. (10740-10967)
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
    4. (22885-23078)
       nnnnnnnnnnnnnnnnnnnnnnnnnntaatctnnnnnnnnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
       nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatggtgttggttaccaacnnnnnnnnnnn
       nnnnnnnnnnnnnn


Comparative Genomics




  1. “Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Carver T, Harris SR, Berriman M, Parkhill J and McQuillan JA Bioinformatics (Oxford, England) 2012;28;4;464-9 PUBMED: 22199388; PMC: 3278759; DOI: 10.1093/bioinformatics/btr703”↩︎

  2. Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), “A greedy algorithm for aligning DNA sequences”, J Comput Biol 2000; 7(1-2):203-14.↩︎

 

A work by Md. Tabassum Hossain Emon

emon.biotech.10th@gmail.com