When running the test data for MHC-I I obtain different clustering results than in the mouse_liver_report.html file.
My results are as follow:
Compared to:
Perhaps this is due to a version difference in gibbscluster using different default arguments ?
Here is the tmp file with the gibbscluster info:
/Users/CS/Downloads/gibbscluster-2.0/bin/gibbs_cluster_1.2.2_DB.Darwin_x86_64 -mhc1 -trash -l 9 -g 1 -ts 1.5 -blf /Users/CS/Downloads/gibbscluster-2.0/data/blosum%i.freq_rownorm -blm 62 -base 2 -bg 1 -i 10 -s 1 -nt 20 -fr 20 -fs 100 -wlc 200 -swt 0 -lambda 0.8 -dlen 4 -ilen 1 -findels 10 -sigma 5 /private/tmp/mhcvizpipe/2022-10-11_12-13-46.252971/gibbs/mouse_liver.txt/H-2-Db/1groups_1738/data/pepdata.txt
# Tue Oct 11 12:14:01 2022
# User: CS
# PWD : /private/tmp/mhcvizpipe/2022-10-11_12-13-46.252971/gibbs/mouse_liver.txt/H-2-Db
# Host: Darwin CRHSJ105816.local 21.6.0 x86_64
# -mhc1 1 Use peptides of fixed length, no window shift
# -trash 1 Use trash cluster to remove outliers
# -l 9 Motif length
# -g 1 Number of initial clusters
# -ts 1.500000 Start temperature
# -blf /Users/CS/Downloads/gibbscluster-2.0/data/blosum%i.freq_rownorm Real value blosum matrix filename
# -blm 62 Blosum matrix number
# -base 2.000000 Baseline value to discard to trash
# -bg 1 [0] Flat (0.05) [1] Precalculated [2] From data
# -i 10 Number of iterations per train example
# -s 1 Seed [-1] Default, [0] Time [>0] Specific seed
# -nt 20 Number of temperature steps
# -fr 20 Interval between Single sequence moves (if -mhc1 == 1)
# -fs 100 Interval between Phase shift moves
# -wlc 200.000000 Weigth on low count
# -swt 0 [0] 1/ns [1] Clustering [2] No sequence weighting
# -lambda 0.800000 Penalty factor for overlapping clusters
# -dlen 4 Max length of deletions
# -ilen 1 Max length of insertions
# -findels 10 Interval between Indel moves
# -sigma 5.000000 Weight on blosum for small cluster confidence
# Command line parameters set to:
# [-l int] 9 Motif length
# [-g int] 1 Number of initial clusters
# [-trash] 1 Use trash cluster to remove outliers
# [-i int] 10 Number of iterations per train example
# [-s int] 1 Seed [-1] Default, [0] Time [>0] Specific seed
# [-f filename] 0 File for frequency matrices
# [-m filename] 0 File for log-odds matrices
# [-a filename] aln.txt File for multiple alignments
# [-pc] 0 Print core of alignment
# [-c filename] core.txt File for core
# [-alp string] ARNDCQEGHILKMFPSTWYV Amino acid alphabet
# [-bg int] 1 [0] Flat (0.05) [1] Precalculated [2] From data
# [-base float] 2.000000 Baseline value to discard to trash
# [-mhc1] 1 Use peptides of fixed length, no window shift
# [-ts float] 1.500000 Start temperature
# [-te float] 0.000010 Final temperature
# [-nt int] 20 Number of temperature steps
# [-ms int] 3 Max phase shift distance
# [-fs int] 100 Interval between Phase shift moves
# [-findels int] 10 Interval between Indel moves
# [-fr int] 20 Interval between Single sequence moves (if -mhc1 == 1)
# [-lambda float] 0.800000 Penalty factor for overlapping clusters
# [-sigma float] 5.000000 Weight on blosum for small cluster confidence
# [-noph] 0 Exclude phase shift move
# [-r float] 5.000000 Scale factor for phase shift moves
# [-wlc float] 200.000000 Weigth on low count
# [-blf filename] /Users/CS/Downloads/gibbscluster-2.0/data/blosum%i.freq_rownorm Real value blosum matrix filename
# [-blm int] 62 Blosum matrix number
# [-cX int] 1 [0] Count X as A, [1] Exclude X from count
# [-v] 0 Verbose mode
# [-debug] 0 Debug model
# [-cthr float] 0.620000 Clustering threshold for sequence weighting
# [-swt int] 0 [0] 1/ns [1] Clustering [2] No sequence weighting
# [-w string] 1,3,1,1,1,1,1,1,3 Weigths on positions
# [-iw] 0 Include weights on positions
# [-noc float] 0.000000 Log-odds score assignment to no count elements
# [-p1a] 0 Allow only Hydrophobic AA at P1
# [-p1l filename] ILVMFYW Allowed letters at P1 [Only with -p1a option]
# [-factor float] 2.885400 Scale factor for matrix 2/log2
# [-cntthr int] 0 Low bound for amino acids counts to include in matrix
# [-p1s] 0 Penalize disallowed P1 amino acids in shift
# [-pkld] 0 Print KLD list (file to -kldf)
# [-kldf string] kldfq.txt Print complete list of KLD values to specified file
# [-kldq int] 1000 Total datapoints when printing KLDs
# [-ilen int] 1 Max length of insertions
# [-dlen int] 4 Max length of deletions
# [-xc] 0 Exclude final check of all peptides to clusters
# Random seed is 1
# Read 332 elements on seqlist /private/tmp/mhcvizpipe/2022-10-11_12-13-46.252971/gibbs/mouse_liver.txt/H-2-Db/1groups_1738/data/pepdata.txt
# Number of temperature steps 20 dt 0.078947
# Back ground frequences
# 0 A 0.07400
# 1 R 0.05200
# 2 N 0.04500
# 3 D 0.05400
# 4 C 0.02500
# 5 Q 0.03400
# 6 E 0.05400
# 7 G 0.07400
# 8 H 0.02600
# 9 I 0.06800
# 10 L 0.09900
# 11 K 0.05800
# 12 M 0.02500
# 13 F 0.04700
# 14 P 0.03900
# 15 S 0.05700
# 16 T 0.05100
# 17 W 0.01300
# 18 Y 0.03200
# 19 V 0.07300
# Read_realblosum done. Alphabet ARNDCQEGHILKMFPSTWYV
# G 0 332
# G 1 0
### Initial alignments weighed KLD sum 0.000000
# Doing temprature step 0 1.500000
# Doing temprature step 1 1.421053
# Doing temprature step 2 1.342106
# Doing temprature step 3 1.263160
# Doing temprature step 4 1.184213
# Doing temprature step 5 1.105266
# Doing temprature step 6 1.026319
# Doing temprature step 7 0.947372
# Doing temprature step 8 0.868425
# Doing temprature step 9 0.789479
# Doing temprature step 10 0.710532
# Doing temprature step 11 0.631585
# Doing temprature step 12 0.552638
# Doing temprature step 13 0.473691
# Doing temprature step 14 0.394744
# Doing temprature step 15 0.315798
# Doing temprature step 16 0.236851
# Doing temprature step 17 0.157904
# Doing temprature step 18 0.078957
# Doing temprature step 19 0.000010
## Sequence alignment for group 0
G 0 0 FQAPNVTFL FQAPNVTFL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 14.648 bgG -1 bgS 2.000 cS 13.048
G 0 1 LALINGTQM LALINGTQM o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 13.062 bgG -1 bgS 2.000 cS 11.462
G 0 2 VSLLNVYYI VSLLNVYYI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 15.539 bgG -1 bgS 2.000 cS 13.939
G 0 3 SSFHFPYL SSF-HFPYL o 0 ip 3 il 1 dp -99 dl -99 Peplist sS 16.355 bgG -1 bgS 2.000 cS 14.755
G 0 4 AGIENKFGLYL AGIENKLYL o 0 ip -99 il -99 dp 6 dl 2 Peplist sS 17.314 bgG -1 bgS 2.000 cS 15.714
G 0 5 ASPEGQDYL ASPEGQDYL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 18.781 bgG -1 bgS 2.000 cS 17.181
G 0 6 SILVNQEVL SILVNQEVL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 18.217 bgG -1 bgS 2.000 cS 16.617
G 0 7 RGVSNGTHV RGVSNGTHV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 14.854 bgG -1 bgS 2.000 cS 13.254
G 0 8 SALRYNTL SALR-YNTL o 0 ip 4 il 1 dp -99 dl -99 Peplist sS 13.269 bgG -1 bgS 2.000 cS 11.669
G 0 9 SAKMNLVVI SAKMNLVVI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 11.840 bgG -1 bgS 2.000 cS 10.240
G 0 10 YAVGNHDFI YAVGNHDFI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 15.728 bgG -1 bgS 2.000 cS 14.128
G 0 11 SALQNAESDRL SALQNAERL o 0 ip -99 il -99 dp 7 dl 2 Peplist sS 21.174 bgG -1 bgS 2.000 cS 19.574
G 0 12 VQPFNYVTL VQPFNYVTL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 18.867 bgG -1 bgS 2.000 cS 17.267
G 0 13 IAPSFVKGF IAPSFVKGF o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 4.706 bgG -1 bgS 2.000 cS 3.106
G 0 14 LNYNFLETL LNYNFLETL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 7.640 bgG -1 bgS 2.000 cS 6.040
G 0 15 AGVINRERM AGVINRERM o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 15.771 bgG -1 bgS 2.000 cS 14.171
G 0 16 VAVYNHYKRI VAVYNHYKI o 0 ip -99 il -99 dp 8 dl 1 Peplist sS 12.482 bgG -1 bgS 2.000 cS 10.882
G 0 17 FSIFNRSIDAF FSIFNIDAF o 0 ip -99 il -99 dp 5 dl 2 Peplist sS 14.690 bgG -1 bgS 2.000 cS 13.090
G 0 18 STIRNADVI STIRNADVI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 16.808 bgG -1 bgS 2.000 cS 15.208
G 0 19 TILEFSQNM TILEFSQNM o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 9.689 bgG -1 bgS 2.000 cS 8.089
G 0 20 SQLRNEVAI SQLRNEVAI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.960 bgG -1 bgS 2.000 cS 11.360
G 0 21 FVISNYREQL FVISNYEQL o 0 ip -99 il -99 dp 6 dl 1 Peplist sS 16.393 bgG -1 bgS 2.000 cS 14.793
G 0 22 KAISNSHYVL KAISNSHYL o 0 ip -99 il -99 dp 8 dl 1 Peplist sS 18.248 bgG -1 bgS 2.000 cS 16.648
G 0 23 STIKNANFV STIKNANFV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 11.743 bgG -1 bgS 2.000 cS 10.143
G 0 24 HSLENSLIDIM HSLENIDIM o 0 ip -99 il -99 dp 5 dl 2 Peplist sS 17.145 bgG -1 bgS 2.000 cS 15.545
G 0 25 ASVINGHTL ASVINGHTL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 16.672 bgG -1 bgS 2.000 cS 15.072
G 0 26 APQGSLGEYL AQGSLGEYL o 0 ip -99 il -99 dp 1 dl 1 Peplist sS 8.737 bgG -1 bgS 2.000 cS 7.137
G 0 27 AAIVDGDRI AAIVDGDRI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 9.418 bgG -1 bgS 2.000 cS 7.818
G 0 28 SNVDLLEEL SNVDLLEEL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 9.675 bgG -1 bgS 2.000 cS 8.075
G 0 29 AVVLNATWL AVVLNATWL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 11.448 bgG -1 bgS 2.000 cS 9.848
G 0 30 RAIYNNMKQFI RAIYNKQFI o 0 ip -99 il -99 dp 5 dl 2 Peplist sS 15.365 bgG -1 bgS 2.000 cS 13.765
G 0 31 TSPVNEKTL TSPVNEKTL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 17.817 bgG -1 bgS 2.000 cS 16.217
G 0 32 TAHYNRERI TAHYNRERI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.560 bgG -1 bgS 2.000 cS 10.960
G 0 33 KSTVNKWTL KSTVNKWTL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 14.457 bgG -1 bgS 2.000 cS 12.857
G 0 34 VSLTHHAGL VSLTHHAGL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 8.192 bgG -1 bgS 2.000 cS 6.592
G 0 35 YSSENISNF YSSENISNF o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 13.912 bgG -1 bgS 2.000 cS 12.312
G 0 36 SSITMSQGGM SSITMSQGM o 0 ip -99 il -99 dp 7 dl 1 Peplist sS 11.577 bgG -1 bgS 2.000 cS 9.977
G 0 37 IAARNQENL IAARNQENL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 14.467 bgG -1 bgS 2.000 cS 12.867
G 0 38 VMPQNQKAI VMPQNQKAI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 14.724 bgG -1 bgS 2.000 cS 13.124
G 0 39 RQPNPPLIL RQPNPPLIL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 4.673 bgG -1 bgS 2.000 cS 3.073
G 0 40 FNLVNNALL FNLVNNALL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 10.438 bgG -1 bgS 2.000 cS 8.838
G 0 41 MNMEITDVL MNMEITDVL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 3.767 bgG -1 bgS 2.000 cS 2.167
G 0 42 SNVVNQANL SNVVNQANL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 16.264 bgG -1 bgS 2.000 cS 14.664
G 0 43 YSLFNVISI YSLFNVISI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.404 bgG -1 bgS 2.000 cS 10.804
G 0 44 YGVSNLQEF YGVSNLQEF o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 16.600 bgG -1 bgS 2.000 cS 15.000
G 0 45 GGLQNIAVV GGLQNIAVV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 11.674 bgG -1 bgS 2.000 cS 10.074
G 0 46 KSLLLLTTL KSLLLLTTL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 11.529 bgG -1 bgS 2.000 cS 9.929
G 0 47 AAPRSFIFL AAPRSFIFL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.369 bgG -1 bgS 2.000 cS 10.769
G 0 48 SAITNVAKI SAITNVAKI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 16.875 bgG -1 bgS 2.000 cS 15.275
G 0 49 RAPSNVSTV RAPSNVSTV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 17.326 bgG -1 bgS 2.000 cS 15.726
G 0 50 TALRNLGSL TALRNLGSL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.840 bgG -1 bgS 2.000 cS 11.240
G 0 51 LSMNPMLL LSM-NPMLL o 0 ip 3 il 1 dp -99 dl -99 Peplist sS 10.791 bgG -1 bgS 2.000 cS 9.191
G 0 52 ISLKNSQEI ISLKNSQEI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 15.721 bgG -1 bgS 2.000 cS 14.121
G 0 53 AMSPVTITTI ASPVTITTI o 0 ip -99 il -99 dp 1 dl 1 Peplist sS 14.228 bgG -1 bgS 2.000 cS 12.628
G 0 54 STITNPSAI STITNPSAI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 15.933 bgG -1 bgS 2.000 cS 14.333
G 0 55 AMYVHAYTL AMYVHAYTL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 9.891 bgG -1 bgS 2.000 cS 8.291
G 0 56 EAIQNSTSI EAIQNSTSI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 13.916 bgG -1 bgS 2.000 cS 12.316
G 0 57 FSPTNYHFL FSPTNYHFL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 22.222 bgG -1 bgS 2.000 cS 20.622
G 0 58 GMKLNLDYL GMKLNLDYL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 9.349 bgG -1 bgS 2.000 cS 7.749
G 0 59 RSPINVESL RSPINVESL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 20.677 bgG -1 bgS 2.000 cS 19.077
G 0 60 AAPTSAARV AAPTSAARV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 8.662 bgG -1 bgS 2.000 cS 7.062
G 0 61 SSPANISSL SSPANISSL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 20.529 bgG -1 bgS 2.000 cS 18.929
G 0 62 FMPPVPITSPI FMPPVPITI o 0 ip -99 il -99 dp 8 dl 2 Peplist sS 7.681 bgG -1 bgS 2.000 cS 6.081
G 0 63 SAPKSISAL SAPKSISAL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 14.189 bgG -1 bgS 2.000 cS 12.589
G 0 64 RALDNDQHL RALDNDQHL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 16.272 bgG -1 bgS 2.000 cS 14.672
G 0 65 ATVSNGPFL ATVSNGPFL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 15.206 bgG -1 bgS 2.000 cS 13.606
G 0 66 VNFEKFWEL VNFEKFWEL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 6.651 bgG -1 bgS 2.000 cS 5.051
G 0 67 FMLALKENI FMLALKENI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 6.852 bgG -1 bgS 2.000 cS 5.252
G 0 68 FSNKNLEEL FSNKNLEEL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 16.179 bgG -1 bgS 2.000 cS 14.579
G 0 69 HSPTNTVHM HSPTNTVHM o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 21.028 bgG -1 bgS 2.000 cS 19.428
G 0 70 AAPTNRQIEIL AAPTNIEIL o 0 ip -99 il -99 dp 5 dl 2 Peplist sS 23.298 bgG -1 bgS 2.000 cS 21.698
G 0 71 GALGNLTVV GALGNLTVV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 11.011 bgG -1 bgS 2.000 cS 9.411
G 0 72 YKYPSDLPYM YKPSDLPYM o 0 ip -99 il -99 dp 2 dl 1 Peplist sS 13.019 bgG -1 bgS 2.000 cS 11.419
G 0 73 KVIKNFTEI KVIKNFTEI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 14.226 bgG -1 bgS 2.000 cS 12.626
G 0 74 RQRENFPNL RQRENFPNL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 15.826 bgG -1 bgS 2.000 cS 14.226
G 0 75 ASVLNVNHI ASVLNVNHI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 15.736 bgG -1 bgS 2.000 cS 14.136
G 0 76 FVIFNNTYI FVIFNNTYI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.436 bgG -1 bgS 2.000 cS 10.836
G 0 77 QQYRFSVIM QQYRFSVIM o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 6.377 bgG -1 bgS 2.000 cS 4.777
G 0 78 STVIHILYL STVIHILYL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 9.927 bgG -1 bgS 2.000 cS 8.327
G 0 79 ISPQNMDIL ISPQNMDIL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 15.208 bgG -1 bgS 2.000 cS 13.608
G 0 80 RSHYNAKHL RSHYNAKHL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.777 bgG -1 bgS 2.000 cS 11.177
G 0 81 AIMPNGDHI AIMPNGDHI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.614 bgG -1 bgS 2.000 cS 11.014
G 0 82 VAPGNQVTL VAPGNQVTL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 18.553 bgG -1 bgS 2.000 cS 16.953
G 0 83 YQYQNIFGPL YQYQNIFGL o 0 ip -99 il -99 dp 8 dl 1 Peplist sS 16.868 bgG -1 bgS 2.000 cS 15.268
G 0 84 RSVLNNQLL RSVLNNQLL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 14.184 bgG -1 bgS 2.000 cS 12.584
G 0 85 KSYVNPTEL KSYVNPTEL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 20.224 bgG -1 bgS 2.000 cS 18.624
G 0 86 AVIQFLERI AVIQFLERI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 10.282 bgG -1 bgS 2.000 cS 8.682
G 0 87 SSPVSHTAV SSPVSHTAV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 13.503 bgG -1 bgS 2.000 cS 11.903
G 0 88 GFADSNSLEI FADSNSLEI o 1 ip -99 il -99 dp -99 dl -99 Peplist sS 6.562 bgG -1 bgS 2.000 cS 4.962
G 0 89 ATYTFIQQL ATYTFIQQL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 13.040 bgG -1 bgS 2.000 cS 11.440
G 0 90 AVLRNQIHV AVLRNQIHV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 11.053 bgG -1 bgS 2.000 cS 9.453
G 0 91 YSPVLQKPKF YSPVLQPKF o 0 ip -99 il -99 dp 6 dl 1 Peplist sS 13.961 bgG -1 bgS 2.000 cS 12.361
G 0 92 QTVENKETL QTVENKETL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 17.361 bgG -1 bgS 2.000 cS 15.761
G 0 93 TTHSNHEVL TTHSNHEVL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 16.355 bgG -1 bgS 2.000 cS 14.755
G 0 94 VAVVNKVDI VAVVNKVDI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.721 bgG -1 bgS 2.000 cS 11.121
G 0 95 SGPALSTALL SGPALSTLL o 0 ip -99 il -99 dp 7 dl 1 Peplist sS 11.904 bgG -1 bgS 2.000 cS 10.304
G 0 96 YAPSIGFPYSL YAPSFPYSL o 0 ip -99 il -99 dp 4 dl 2 Peplist sS 16.724 bgG -1 bgS 2.000 cS 15.124
G 0 97 LGPINQWWL LGPINQWWL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 15.068 bgG -1 bgS 2.000 cS 13.468
G 0 98 QVYTFTERM QVYTFTERM o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 8.111 bgG -1 bgS 2.000 cS 6.511
G 0 99 VLIPKLPQL VLIPKLPQL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 2.737 bgG -1 bgS 2.000 cS 1.137
G 0 100 YSPTGKEFV YSPTGKEFV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 13.996 bgG -1 bgS 2.000 cS 12.396
G 0 101 EAILNKYYL EAILNKYYL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 13.722 bgG -1 bgS 2.000 cS 12.122
G 0 102 VGVVSVEFI VGVVSVEFI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 8.568 bgG -1 bgS 2.000 cS 6.968
G 0 103 SALRFLNL SALRFL-NL o 0 ip 6 il 1 dp -99 dl -99 Peplist sS 13.777 bgG -1 bgS 2.000 cS 12.177
G 0 104 VQLENQMVL VQLENQMVL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 16.420 bgG -1 bgS 2.000 cS 14.820
G 0 105 LGLSNLTHL LGLSNLTHL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 17.485 bgG -1 bgS 2.000 cS 15.885
G 0 106 SAPLSPLKF SAPLSPLKF o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 9.126 bgG -1 bgS 2.000 cS 7.526
G 0 107 VSNFSKDLL VSNFSKDLL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 2.910 bgG -1 bgS 2.000 cS 1.310
G 0 108 GSIINYMVVM GSIINYVVM o 0 ip -99 il -99 dp 6 dl 1 Peplist sS 14.418 bgG -1 bgS 2.000 cS 12.818
G 0 109 IAPLFYSL IAPL-FYSL o 0 ip 4 il 1 dp -99 dl -99 Peplist sS 10.722 bgG -1 bgS 2.000 cS 9.122
G 0 110 KGIGNKTEI KGIGNKTEI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 13.042 bgG -1 bgS 2.000 cS 11.442
G 0 111 SAPTFINF SAPTFI-NF o 0 ip 6 il 1 dp -99 dl -99 Peplist sS 15.740 bgG -1 bgS 2.000 cS 14.140
G 0 112 VSPRLTFL VSPR-LTFL o 0 ip 4 il 1 dp -99 dl -99 Peplist sS 15.416 bgG -1 bgS 2.000 cS 13.816
G 0 113 SSLHNLTFL SSLHNLTFL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 19.636 bgG -1 bgS 2.000 cS 18.036
G 0 114 SSIVNKEGL SSIVNKEGL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 19.998 bgG -1 bgS 2.000 cS 18.398
G 0 115 SAVISLEGKPL SAVISLEGL o 0 ip -99 il -99 dp 8 dl 2 Peplist sS 11.037 bgG -1 bgS 2.000 cS 9.437
G 0 116 VAMANTVAM VAMANTVAM o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 11.519 bgG -1 bgS 2.000 cS 9.919
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G 0 276 FGPDLKLAPRM FGPKLAPRM o 0 ip -99 il -99 dp 3 dl 2 Peplist sS 12.020 bgG -1 bgS 2.000 cS 10.420
G 0 277 YVVDNIDHL YVVDNIDHL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 17.192 bgG -1 bgS 2.000 cS 15.592
G 0 278 YAVSNHSGTTM YAVSNHTTM o 0 ip -99 il -99 dp 6 dl 2 Peplist sS 21.625 bgG -1 bgS 2.000 cS 20.025
G 0 279 VSVTNLEEL VSVTNLEEL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 20.153 bgG -1 bgS 2.000 cS 18.553
G 0 280 KVMKNVSEI KVMKNVSEI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 9.426 bgG -1 bgS 2.000 cS 7.826
G 0 281 RQLENTEHM RQLENTEHM o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 22.550 bgG -1 bgS 2.000 cS 20.950
G 0 282 KAVKNFTDV KAVKNFTDV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 13.621 bgG -1 bgS 2.000 cS 12.021
G 0 283 FGLRNLERLYL FGLRNLEYL o 0 ip -99 il -99 dp 7 dl 2 Peplist sS 21.330 bgG -1 bgS 2.000 cS 19.730
G 0 284 VGPELHHKLL VGPELHHKL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.053 bgG -1 bgS 2.000 cS 10.453
G 0 285 TSVSNFLVM TSVSNFLVM o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 16.273 bgG -1 bgS 2.000 cS 14.673
G 0 286 VSPSNEQVL VSPSNEQVL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 19.655 bgG -1 bgS 2.000 cS 18.055
G 0 287 AAVVGATHL AAVVGATHL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 11.876 bgG -1 bgS 2.000 cS 10.276
G 0 288 AAVENLKNI AAVENLKNI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 16.552 bgG -1 bgS 2.000 cS 14.952
G 0 289 QAIKNGQAL QAIKNGQAL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 14.052 bgG -1 bgS 2.000 cS 12.452
G 0 290 AQYNFILV AQY-NFILV o 0 ip 3 il 1 dp -99 dl -99 Peplist sS 11.725 bgG -1 bgS 2.000 cS 10.125
G 0 291 SNYERLESL SNYERLESL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 11.645 bgG -1 bgS 2.000 cS 10.045
G 0 292 FSPINWDDL FSPINWDDL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 20.579 bgG -1 bgS 2.000 cS 18.979
G 0 293 AALANATVI AALANATVI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 15.392 bgG -1 bgS 2.000 cS 13.792
G 0 294 SALDWWPKI SALDWWPKI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 9.493 bgG -1 bgS 2.000 cS 7.893
G 0 295 AAPVSGPRL AAPVSGPRL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 13.468 bgG -1 bgS 2.000 cS 11.868
G 0 296 NAPQNPESKL NAPQNPESL o 0 ip -99 il -99 dp 8 dl 1 Peplist sS 22.001 bgG -1 bgS 2.000 cS 20.401
G 0 297 TAYAFHFL TAYAFH-FL o 0 ip 6 il 1 dp -99 dl -99 Peplist sS 9.406 bgG -1 bgS 2.000 cS 7.806
G 0 298 ATILNLERV ATILNLERV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.976 bgG -1 bgS 2.000 cS 11.376
G 0 299 YTIQNRVDI YTIQNRVDI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.744 bgG -1 bgS 2.000 cS 11.144
G 0 300 TSPVNPAVF TSPVNPAVF o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 18.221 bgG -1 bgS 2.000 cS 16.621
G 0 301 GAIVNGKVL GAIVNGKVL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 12.858 bgG -1 bgS 2.000 cS 11.258
G 0 302 AAMLLQQVM AAMLLQQVM o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 11.184 bgG -1 bgS 2.000 cS 9.584
G 0 303 KQAQNIVTL KQAQNIVTL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 15.672 bgG -1 bgS 2.000 cS 14.072
G 0 304 ISPLFAEL ISPLFAE-L o 0 ip 7 il 1 dp -99 dl -99 Peplist sS 13.032 bgG -1 bgS 2.000 cS 11.432
G 0 305 TGLRNGSFL TGLRNGSFL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 14.051 bgG -1 bgS 2.000 cS 12.451
G 0 306 QSIAFISRL QSIAFISRL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 7.310 bgG -1 bgS 2.000 cS 5.710
G 0 307 SSVKNVPENL SSVKNPENL o 0 ip -99 il -99 dp 5 dl 1 Peplist sS 22.960 bgG -1 bgS 2.000 cS 21.360
G 0 308 SSIVAQTAGI SSIVAQTAI o 0 ip -99 il -99 dp 8 dl 1 Peplist sS 10.007 bgG -1 bgS 2.000 cS 8.407
G 0 309 RAIKNDSVV RAIKNDSVV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 10.615 bgG -1 bgS 2.000 cS 9.015
G 0 310 KARELWDSI KARELWDSI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 4.535 bgG -1 bgS 2.000 cS 2.935
G 0 311 YIHINIGAL YIHINIGAL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 6.379 bgG -1 bgS 2.000 cS 4.779
G 0 312 YQLLLKEML YQLLLKEML o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 7.528 bgG -1 bgS 2.000 cS 5.928
G 0 313 AALEFLNRF AALEFLNRF o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 9.003 bgG -1 bgS 2.000 cS 7.403
G 0 314 SRPGHIETF SRPGHIETF o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 6.913 bgG -1 bgS 2.000 cS 5.313
G 0 315 VIVPHIVNL VIVPHIVNL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 5.553 bgG -1 bgS 2.000 cS 3.953
G 0 316 GNYKWINYL GNYKWINYL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 5.974 bgG -1 bgS 2.000 cS 4.374
G 0 317 AGYMYTQLM AGYMYTQLM o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 4.321 bgG -1 bgS 2.000 cS 2.721
G 0 318 TSYDKRYVI TSYDKRYVI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 5.741 bgG -1 bgS 2.000 cS 4.141
G 0 319 SDFTVFERI SDFTVFERI o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 2.660 bgG -1 bgS 2.000 cS 1.060
G 0 320 VAFIFNQKF VAFIFNQKF o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 4.479 bgG -1 bgS 2.000 cS 2.879
G 0 321 IGYPFLVSV IGYPFLVSV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 4.040 bgG -1 bgS 2.000 cS 2.440
G 0 322 KVLRFIAEV KVLRFIAEV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 3.425 bgG -1 bgS 2.000 cS 1.825
G 0 323 VSFEKKVQV VSFEKKVQV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 4.237 bgG -1 bgS 2.000 cS 2.637
G 0 324 KLLALKDFM KLLALKDFM o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 1.743 bgG -1 bgS 2.000 cS 0.143
G 0 325 NNISSTVTV NNISSTVTV o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 3.122 bgG -1 bgS 2.000 cS 1.522
G 0 326 NSIVDQRDL NSIVDQRDL o 0 ip -99 il -99 dp -99 dl -99 Peplist sS 2.417 bgG -1 bgS 2.000 cS 0.817
## Trash cluster (5 outliers)
#Trash1 RSAATYLTV Peplist
#Trash2 IGIDKFGEI Peplist
#Trash3 MGFGAFAAL Peplist
#Trash4 VAYWHILSV Peplist
#Trash5 AAGVGDMVM Peplist
# group 0, size 327: Final KLD sum after 66400 epochs - 12.026946
# Trash cluster: removed 5 outliers
#
# Final number of non-empty clusters: 1
### Final KLD sum after 66400 iterations: 12.026946`
When running the test data for MHC-I I obtain different clustering results than in the mouse_liver_report.html file.
My results are as follow:
Compared to:
Perhaps this is due to a version difference in gibbscluster using different default arguments ?
Here is the tmp file with the gibbscluster info: