Example
In this simple demonstration, you will see how to calculate ZBLMIp (Z score of the corrected MIp using BLOSUM62 pseudo frequencies) for a Pfam
MSA from the Julia REPL or using a MIToS script in the system command line.
MIToS in the Julia REPL
If you load the Pfam module from MIToS, you will get access to a set of functions that work with Pfam MSAs. In this case, we are going to use it for download a Stockholm MSA from the Pfam website and read it into Julia.
using MIToS.Pfam
pfam_file = downloadpfam("PF10660")
msa = read(pfam_file, Stockholm, generatemapping=true, useidcoordinates=true)AnnotatedMultipleSequenceAlignment with 1001 annotations : 487×64 Named Array{MIToS.MSA.Residue,2}
Seq ╲ Col │ 32 35 36 37 38 … 103 104 105 106 107
─────────────────────────┼────────────────────────────────────────────────────
A0A1L8HM45_XENLA/102-167 │ M E S L A … K K K Q Q
A0A2I2Y8P5_GORGO/9-41 │ - - - - - K D H R N
W5UKX1_ICTPU/1-66 │ - E T I S K R K K -
A0A182JXL2_9DIPT/1-64 │ M Q L L S E A R - -
F6TSD5_XENTR/1-66 │ M E S I A K K K Q Q
A0A158NWR3_ATTCE/11-73 │ M E P I A R - - - -
A0A1J1J3N7_9DIPT/1-64 │ M E L I S A S - - -
A0A2I3LDM8_PAPAN/42-76 │ - - - - - K K K Q Q
A0A091D4B4_FUKDA/1-66 │ M E S V A K K K Q Q
⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋱ ⋮ ⋮ ⋮ ⋮ ⋮
G3H4L8_CRIGR/2-34 │ - - - - - K E N R -
G3SVU7_LOXAF/8-41 │ - - - - - K D H R -
A0A1S3IS31_LINUN/1-64 │ M E T V S S K K K -
A0A484E3E9_BRELC/1-56 │ M D A I R - - - - -
A0A194RSG1_PAPMA/1-63 │ M Y F V S - - - - -
A0A218UPM6_9PASE/1-66 │ - E T L A K K K Q Q
H0VMN3_CAVPO/8-41 │ - - - - - K D H R N
A0A2K5YPF8_MANLE/3-41 │ - - - - - K D H R N
A0A1A6GRS4_NEOLE/34-94 │ - - - - - … K D N R -Generation of sequence and column mappings The keyword argument generatemapping of read allows to generate sequence and column mappings for the MSA. Column mapping is the map between of each column on the MSA object and the column number in the file. Sequence mappings will use the start and end coordinates in the sequence ids for enumerate each residue in the sequence if useidcoordinates is true.
You can plot this MSA and other MIToS’ objects using the Plots package. The installation of Plots is described in the Installation section of this site:
using Plots
gr()
plot(msa)/juliateam/.julia/packages/GR/8mv9N/src/../deps/gr/bin/gksqt: error while loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: No such file or directory connect: Connection refused GKS: can't connect to GKS socket application GKS: Open failed in routine OPEN_WS GKS: GKS not in proper state. GKS must be either in the state WSOP or WSAC in routine ACTIVATE_WS
The Information module of MIToS has functions to calculate measures from the Information Theory, such as Entropy and Mutual Information (MI), on a MSA. In this example, we will estimate covariation between columns of the MSA with a corrected MI that use the BLOSUM62 matrix for calculate pseudo frequencies (BLMI).
using MIToS.Information
ZBLMIp, BLMIp = BLMI(msa)
ZBLMIp # shows ZBLMIp scores63×63 Named PairwiseListMatrices.PairwiseListMatrix{Float64,false,Array{Float64,1}}
Col1 ╲ Col2 │ 35 36 … 106 107
────────────┼──────────────────────────────────────────────────────────
35 │ NaN 0.0563188 … -0.100055 -0.23808
36 │ 0.0563188 NaN 0.155435 -0.464417
37 │ 0.00851406 0.00603174 -0.262926 -0.287343
38 │ 0.0583976 0.00799689 -0.163582 -0.458561
39 │ -0.0814246 0.123884 -0.0256342 -0.505752
40 │ 0.0681652 0.0598754 -0.0854044 -0.366635
41 │ 0.00506371 -0.0598257 0.0281494 -0.2211
42 │ 0.165036 -0.0603626 0.095943 -0.274653
43 │ -0.00736844 -0.0556297 -0.0824943 -0.411009
⋮ ⋮ ⋮ ⋱ ⋮ ⋮
99 │ -0.0721807 0.0460013 -0.0297737 0.153822
100 │ 0.143868 0.104842 -0.104186 -0.336944
101 │ 0.0214702 0.150564 -0.214496 0.252194
102 │ -0.0838159 -0.11169 0.070556 0.124214
103 │ 0.0533966 0.0834249 -0.06889 -0.267319
104 │ -0.0662117 -0.0165336 -0.0653821 -0.102652
105 │ 0.174843 0.296709 -0.219076 0.139308
106 │ -0.100055 0.155435 NaN 0.116601
107 │ -0.23808 -0.464417 … 0.116601 NaNOnce the Plots package is installed and loaded, you can use its capabilities to visualize this results:
heatmap(ZBLMIp, yflip=true, c=:grays)┌ Warning: Attribute alias `ratio` detected in the user recipe defined for the signature (::NamedArrays.NamedArray{Float64,2,PairwiseListMatrices.PairwiseListMatrix{Float64,false,Array{Float64,1}},Tuple{OrderedCollections.OrderedDict{String,Int64},OrderedCollections.OrderedDict{String,Int64}}}). To ensure expected behavior it is recommended to use the default attribute `aspect_ratio`.
└ @ Plots ~/.julia/packages/Plots/ViMfq/src/pipeline.jl:15
/juliateam/.julia/packages/GR/8mv9N/src/../deps/gr/bin/gksqt: error while loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: No such file or directory
connect: Connection refused
GKS: can't connect to GKS socket application
GKS: Open failed in routine OPEN_WS
GKS: GKS not in proper state. GKS must be either in the state WSOP or WSAC in routine ACTIVATE_WS
MIToS in system command line
Calculate ZBLMIp on the system shell is easy using the MIToS script called BLMI.jl. This script reads a MSA file, and writes a file with the same base name of the input but with the .BLMI.csv extension.
BLMI.jl PF14972.stockholm.gz