Tutorial

In the sample folder are available all input and output files used in this tutorial.

Target/Template alignment

Supposing you have already found a template candidate, you need to align it against your target sequence. In this dummy example we take the sequences of two homologous proteins both endowed with 3D structure. That allows us to compare different type of Victor alignments with the "exact" one derived from the structural alignment.

The two proteins are:

• Target = 2ANL (chain A)
• Template = 1DP5 (chain A)

The two structure superimpose quite well (RMSD 2.03 A) considering the low level of sequence identity (28.06%). This is the resulting sequence alignment after the 3D alignment done by FATCAT:

The subali application let you choose from very different type of algorithms, strategies and parameters. The fist step is to create a file (i.e. pair.fasta) including both the target and template Fasta sequences together like that:

>2ANL:A Target
SENDVIELDDVANLMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSIGCSTKHLYDSSKSKSYEKDGTKVEITYGSG
TVRGFFSKDLVTLGYLSLPYKFIEVTDTDDLEPLYTAAEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDQALFTFYLPV
HDKHSGYLTIGGIEEKFYEGELTYEKLNHDLFWQVDLDVNFGKTSMEKANVIVDSGTSTITAPTSFINKFFKDLNVIKVP
FLPFYITTCNNKDMPTLEFKSANNTYTLEPEYYMEPLLDIDDTLCMLYILPVDIDKNTFILGDPFMRKYFTVFDYDKESI
GFAVAKN
>1DP5:A Template
GGHDVPLTNYLNAQYYTDITLGTPPQNFKVILDTGSSNLWVPSNECGSLACFLHSKYDHEASSSYKANGTEFAIQYGTGS
LEGYISQDTLSIGDLTIPKQDFAEATSEPGLTFAFGKFDGILGLGYDTISVDKVVPPFYNAIQQDLLDEKRFAFYLGDTS
KDTENGGEATFGGIDESKFKGDITWLPVRRKAYWEVKFEGIGLGDEYAELESHGAAIDTGTSLITLPSGLAEMINAEIGA
KKGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPYDYTLEVSGSCISAITPMDFPEPVGPLAIVGDAFLRKYYSIYDLGN
NAVGLAKAI

Sequence to sequence alignment

Supposing we call the input file with the target and template sequences pair.fasta than by running the following command you obtain a basic alignment with the default parameters (see Features):

subali --in pair.fasta

The resulting alignment is this:

Profile to profile alignment

subali --in pair.fasta --pro1 2anl_A.psi --pro2 1dp5_A.psi