The goal of pfamscanr is to …
You can download the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("USCbiostats/pfamscanr")This is an example extracted directly from the website https://www.ebi.ac.uk/Tools/pfa/pfamscan/
library(pfamscanr)
ans <- pfamscan(
fasta_str = ">sp|P35858|ALS_HUMAN OS=Homo sapiens GN=IGFALS PE=1 SV=1
MALRKGGLALALLLLSWVALGPRSLEGADPGTPGEAEGPACPAACVCSYDDDADEL
SVFCSSRNLTRLPDGVPGGTQALWLDGNNLSSVPPAAFQNLSSLGFLNLQGGQLGS
LEPQALLGLENLCHLHLERNQLRSLALGTFAHTPALASLGLSNNRLSRLEDGLFEG
LGSLWDLNLGWNSLAVLPDAAFRGLGSLRELVLAGNRLAYLQPALFSGLAELRELD
LSRNALRAIKANVFVQLPRLQKLYLDRNLIAAVAPGAFLGLKALRWLDLSHNRVAG
LLEDTFPGLLGLRVLRLSHNAIASLRPRTFKDLHFLEELQLGHNRIRQLAERSFEG
LGQLEVLTLDHNQLQEVKAGAFLGLTNVAVMNLSGNCLRNLPEQVFRGLGKLHSLH
LEGSCLGRIRPHTFTGLSGLRRLFLKDNGLVGIEEQSLWGLAELLELDLTSNQLTH
LPHRLFQGLGKLEYLLLSRNRLAELPADALGPLQRAFWLDVSHNRLEALPNSLLAP
LGRLRYLSLRNNSLRTFTPQPPGLERLWLEGNPWDCGCPLKALRDFALQNPSAVPR
FVQAICEGDDCQPPAYTYNNITCASPPEVVGLDLRDLSEAHFAPC",
email = "[email protected]",
httr::config(connecttimeout=60)
)ans
#> model_length
#> 1 28
#> 2 61
#> 3 61
#> 4 61
#> 5 61
#> 6 61
#> align
#> 1 #HMM aCPrpChCs......alvVnCsergLtavPrdlP, #MATCH aCP+ C+Cs +l+V+Cs+r+Lt++P+++P, #PP 7*******************************99, #SEQ ACPAACVCSydddadELSVFCSSRNLTRLPDGVP
#> 2 #HMM sLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL, #MATCH L L+ N+l+s+++ aF++ls+L L+L +l +l+p+a+ gL++L +L+L++N+L, #PP 6789***************************************************98, #SEQ ALWLDGNNLSSVPPAAFQNLSSLGFLNLQGGQLGSLEPQALLGLENLCHLHLERNQL
#> 3 #HMM pnLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL, #MATCH p L sL LsnNrl+ l+d+ F+gl +L L+L+ N+l +l af+gL sLr+L L gNrL, #PP 6799*******************************************************98, #SEQ PALASLGLSNNRLSRLEDGLFEGLGSLWDLNLGWNSLAVLPDAAFRGLGSLRELVLAGNRL
#> 4 #HMM nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNr, #MATCH +L++LdLs+N l +++ +F +l++L+ L+L +Nl+ + pgaf gL++Lr+LdLs+Nr, #PP 59********************************************************8, #SEQ ELRELDLSRNALRAIKANVFVQLPRLQKLYLDRNLIAAVAPGAFLGLKALRWLDLSHNR
#> 5 #HMM LtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL, #MATCH L++L Ls+N + sl++ +Fk+l+ L++L+L++N+++ l +++f+gL +L+ L+L++N+L, #PP 99*******************************************************98, #SEQ LRVLRLSHNAIASLRPRTFKDLHFLEELQLGHNRIRQLAERSFEGLGQLEVLTLDHNQL
#> 6 #HMM nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL, #MATCH +L+sL+L + l +++++F+gls+L+ L L++N l +++++++gL+ L +LdL++N+L, #PP 69********************************************************98, #SEQ KLHSLHLEGSCLGRIRPHTFTGLSGLRRLFLKDNGLVGIEEQSLWGLAELLELDLTSNQL
#> env.to env.from name acc sig evalue
#> 1 73 40 LRRNT PF01462.18 1 1.5e-09
#> 2 134 74 LRR_8 PF13855.6 1 4.6e-10
#> 3 206 146 LRR_8 PF13855.6 1 5.1e-14
#> 4 278 219 LRR_8 PF13855.6 1 1.5e-16
#> 5 350 290 LRR_8 PF13855.6 1 4.2e-16
#> 6 446 386 LRR_8 PF13855.6 1 5e-13
#> desc hmm.to hmm.from act_site type bits
#> 1 Leucine rich repeat N-terminal domain 28 1 NA Family 37.3
#> 2 Leucine rich repeat 61 5 NA Repeat 39.1
#> 3 Leucine rich repeat 61 1 NA Repeat 51.8
#> 4 Leucine rich repeat 60 2 NA Repeat 59.9
#> 5 Leucine rich repeat 61 3 NA Repeat 58.4
#> 6 Leucine rich repeat 61 2 NA Repeat 48.6
#> clan seq.to seq.from seq.name
#> 1 No_clan 73 40 sp|P35858|ALS_HUMAN
#> 2 CL0022 134 78 sp|P35858|ALS_HUMAN
#> 3 CL0022 206 146 sp|P35858|ALS_HUMAN
#> 4 CL0022 277 219 sp|P35858|ALS_HUMAN
#> 5 CL0022 350 292 sp|P35858|ALS_HUMAN
#> 6 CL0022 446 387 sp|P35858|ALS_HUMAN