Homework 8

Q1: Could you do the multiple sequence alignment for this DNA binding region only? You need to use at least 10 DNA binding regions from similar proteins to make a color-coded plot.

Ans:

Selected Sequence(s)
HMG-BOX,
OS MUS MUSCULUS (MOUSE).,
sp_O18896_SOX9_PIG TRANSCRIPTION FACTOR SOX-9_gi_2554931 (AF029696) SOX-9 protein [Sus scrofa],
gnl_PID_d1026224 (AB012236) SOX9 [Gallus gallus],
sp_P48434_SOX9_CHICK TRANSCRIPTION FACTOR SOX-9_gi_1589736 (U12533) Sox9 transcription factor [Gallus
gallus],
sp_P35713_SX18_HUMAN TRANSCRIPTION FACTOR SOX-18_gi_107710_pir__S22941 sex-determining protein
SOX-8 - human (fragment)_gi_938233 (X65664) SOX-8 [Homo sapiens],
(L29086) HMG-box transcription factor [Mus musculus],
dbj__D83649_1 (D83649) xSox7 protein [Xenopus laevis],

gnl_PID_e1169910 (AJ001742) Xsox17-beta protein [Xenopus laevis],
sp_Q61473_SX17_MOUSE TRANSCRIPTION FACTOR SOX-17_gi_1487868_gnl_PID_d1009055 (D49474) HMG-box
transcription factor [Mus musculus],
gnl_PID_e1169908 (AJ001730) Xsox17-alpha [Xenopus laevis],
pir__JC4238 HMG-box transcription factor - mouse

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Q2: Could you also do the phylogenetic analysis for him?

Ans:

       Sequence Information

Sequence 1: HMG-BOX - Seq1         545 aa

Sequence 2: MOUSE - Seq2               545 aa

Sequence 3: AF029696 - Seq3             545 aa

Sequence 4: AB012236 - Seq4             545 aa

Sequence 5: U12533 - Seq5                  545 aa

Sequence 6: fragment - Seq6                 545 aa

Sequence 7: L29086 - Seq7                   545 aa

Sequence 8: D83649 - Seq8                   545 aa

Sequence 9: AJ001742 - Seq9                545 aa

Sequence 10: D49474 - Seq10                545 aa

Sequence 11: AJ001730 - Seq11             545 aa

Sequence 12: pir JC4238 HMG - Seq12 545 aa

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PHYLIP rooted tree -Phenogram

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PHYLIP unrooted tree

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