Bioinformatics HW#9

1. Could you do multiple sequence alignment for Jason Lee for the protein that you translated for him on homework 7? Please select the proteins from at least seven different species to show color-coded plot of alignment .

The protein is Lycopersicon pennellii (potatoe) lipid transfer protein 2 (LpLTP2). Here's the colored-plot of multiple aligmnets, for this protein (labeled as "NLT2_POTAT") and 8 similar proteins from different species:

Sequence	Fasta label (*)		Workbench label (**)
---------------------------------------------------------------------------------------------
  1		NL11_PARJU		OS PARIETARIA JUDAICA.,
  2		NLTP_AMACA		OS AMARANTHUS CAUDATUS (LOVE-LIES-BLEEDING) (INCA-WHEAT).,
  3		NLTP_PINTA		OS PINUS TAEDA (LOBLOLLY PINE).,
  4		NLTP_BETVU		OS BETA VULGARIS (SUGAR BEET).,
  5		NLT1_GOSHI		OS GOSSYPIUM HIRSUTUM (UPLAND COTTON).,
  6		NLTP_SPIOL		OS SPINACIA OLERACEA (SPINACH).,
  7		NLT2_TOBAC		OS NICOTIANA TABACUM (COMMON TOBACCO).,
  8		NLT2_LYCES		OS LYCOPERSICON ESCULENTUM (TOMATO).,
  9		NLT2_POTATOE		Lycopersicon pennellii (POTATOE)

2. Please also do the phylogenetic analysis for him.

The rooted phenogram:

The unrooted phenogram: