Difference between revisions of "Tutorial"
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==Profile to profile alignment== | ==Profile to profile alignment== | ||
| + | Most of the time including evolutionary information helps improving the alignment quality. In this example we used command line PsiBlast to calculate profiles both for the target and the template sequences. | ||
| + | The profiles have to be generated in a specific format using the option '''-outfmt 4''' (6 in older versions of Blast, see [[Features]]). In our case the commands are: | ||
| + | |||
| + | psiblast -num_iterations 3 -db /db/blastdb/nr90 -query 2anl_A.fasta -out 2anl_A.psi -outfmt 4 | ||
| + | |||
| + | psiblast -num_iterations 3 -db /db/blastdb/nr90 -query 1dp5_A.fasta -out 1dp5_A.psi -outfmt 4 | ||
| − | + | Then to generate the alignment simply run: | |
| + | subali --in pair.fasta --pro1 2anl_A.psi --pro2 1dp5_A.psi | ||
| + | [[File:3d_align.png|700px]] | ||
=Evaluate 3D models= | =Evaluate 3D models= | ||
=Build loops= | =Build loops= | ||
Revision as of 12:33, 20 August 2014
In the sample folder are available all input and output files used in this tutorial.
Contents
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
Most of the time including evolutionary information helps improving the alignment quality. In this example we used command line PsiBlast to calculate profiles both for the target and the template sequences. The profiles have to be generated in a specific format using the option -outfmt 4 (6 in older versions of Blast, see Features). In our case the commands are:
psiblast -num_iterations 3 -db /db/blastdb/nr90 -query 2anl_A.fasta -out 2anl_A.psi -outfmt 4 psiblast -num_iterations 3 -db /db/blastdb/nr90 -query 1dp5_A.fasta -out 1dp5_A.psi -outfmt 4
Then to generate the alignment simply run:
subali --in pair.fasta --pro1 2anl_A.psi --pro2 1dp5_A.psi
