Histone H4  family

 

Hypotheses: The Histone H4 gene contains same palindromes in different organisms.

We wanted to find out if organisms have the same ancestor for this gene by checking

the palindrome fingerprint of the organisms.

 

We tested the hypotheses by running the algorithm on 8 different organisms with the same set of parameters:

 Length=8, Gap=3, Mismatch=2

(The outcome of other sets of parameters was: no palindromes or too many, making it hard to compare between the different organisms.)

 

Since each organism carries genes that have changed by evolution, the palindromes we found are not exact match. To score the similarity between the palindromes we used ALIGN Query at the site: http://www2.igh.cnrs.fr/bin/align-guess.cgi).

The maximum score is 100% identity, so we chose to report only significant scores that are 50% higher. 

 

 

Search results summary .  (The parameters are:  length=8, gap=3, mismatch=2)

 

Organism

# of pal expected

# of pal found

N – sequence length

Solanum chacoense

(Eukaryota)

6.9

1

425

TTCTGTAA

AAGACATA

 

Drosophila melanogaster

 

13

3

786

CGAACGAA            TTTGTACA                 TTGTACAG

GCTTGCTA           AAACATGT                 AACATGTC                 

 

Arabidopsis thaliana

(Eukaryota)

9

2

549

ATTCTCTC       GTCTCATC

TAAAAGAG       CAGAGGAG  

 

Rattus norvegicus

 

9.76

1

594

ACCATGTC

TGGTGCAG

 

Homo sapiens

 

14.32

5

864

GGGGGCGC   CACAGCCA  CACTTGAC  AAAGACTT   GGGGCGCT    

CCACCGCG   GTGTAGGT  GTGAAATG  TTGCTGAA   CACCGCGA     

Chicken

10.9

22

661

Eucalyptus globulus

 

7.35

3

451

AGCCGGCG       GGATCAGC        GATCAGCG    

TCTAGTCG       CTAGTCGG        TCGGCGGC

                       

Corn

15.77

15

949

 

 

 

Alignment results

 

We used only one “side” of the pal’ in order to align between 2 different pal’,

 since two “sides” complement each other.

 

 

Score

Palindrome # 1

Palindrome # 2

77.8%

 

TTCTGTAA

 

Solanum chacoense

 

TTTGTACA

 

Drosophila melanogaster

62.5%

CACAGCCA

 

Homo sapiens

CGCCGCCT

 

Chicken

 

62.5%

GGCGAGAG

 

Corn

GGCGCGGC

 

Chicken

55.6%

GGGGGCGC

 

Homo sapiens

 

AGCCGGCG

 

Eucalyptus globulus

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Conclusions:

 

We found only a few couples of palindromes that have 50% identity or higher, from this we can assume there is a slight resemblance between the organisms. 

We cannot determine if there is a common ancestor based on these results.