General Category > General Discussion
"Affinity Profile"
mina:
Hi,
I am a new user of REDUCE suite.
Is there anybody to help me in using "Affinity Profile". How could we find the PSAM file for our DNA queries to run the computational calculation of binding affinity.
Best Regards,
Mina
xiangjun:
Hi Mina,
Thanks for using the REDUCE Suite and for posting your questions on the Forum.
Type AffinityProfile -h, and try the examples, on how to use the program. PSAM is a MatrixREDUCE-specific term and can be derived from running MatrixREDUCE. You may also run Convert2PSAM to convert commonly-used formats to PSAM. As with AffinityProfile -h, you can type -h or --help of these programs for helpful information with examples.
You may also want to try other (more sophisticated) software tools developed by the Bussemaker Lab.
Best regards,
Xiang-Jun
ElliotRi:
--- Quote from: xiangjun on January 01, 2019, 11:46:54 am ---Hi Mina,
Thanks for using the electric log splitters and for posting your questions on the Forum.
Type AffinityProfile -h, and try the examples, on how to use the program. PSAM is a MatrixREDUCE-specific term and can be derived from running MatrixREDUCE. You may also run Convert2PSAM to convert commonly-used formats to PSAM. As with AffinityProfile -h, you can type -h or --help of these programs for helpful information with examples.
You may also want to try other (more sophisticated) software tools developed by the Bussemaker Lab.
Best regards,
Xiang-Jun
--- End quote ---
What examples of how to use the program are you exactly referring to, Xiang-Jun?
xiangjun:
Please see http://reducesuite.bussemakerlab.org/documentation/affinityprofile/ which you get by "AffinityProfile -h".
Best regards,
Xiang-Jun
azadeh.s:
Hello
I'am also novice for using your great package REDUCE_Suit.
I'm interested to study the affinity profile for a vary famous gene COL1A1( I downloded COL1A1 from Ensembel database) I tried to understand the dynamic of affinity profile for a transcription factor Sp1 through its binding site for both wild and mutant COL1A1 genes .
To start my study I ran the commande :
AffinityProfile \
-prefix=aff_ \
-threshold=0 \
-psam=../../Desktop/source/REDUCE-Suite-v2.2/examples/AffinityProfile/psam_001.xml \
-sequence=sequence_COL1A1.fasta
As a Psam matrix, I used the matrix given in your example.
But then I don't understand the result.
cat seq_psam.dat
psam_001.xml
NM_000088.3 0.0301094
####################
cat AffinityProfile.log
sequence file: sequence_COL1A1.fasta cut-off: 0
reading in sequences from file [sequence_COL1A1.fasta]
reading in PSAM ../../Desktop/source/REDUCE-Suite-v2.2/examples/AffinityProfile/psam_001.xml [1/1]
[ 1]: ../../Desktop/source/REDUCE-Suite-v2.2/examples/AffinityProfile/psam_001.xml (forward); pmax=0.025626
Time used: 00:00:00:00
#################
cat aff_psam_001.xml
NM_000088.3 0.0301094 1:2.78962e-104 2:2.8034e-101 3:2.508e-07 4:2.97891e-94 5:3.73255e-103 6:4.75891e-116 7:6.73541e-70 8:6.52039e-71 9:5.81238e-65 10:4.04049e-53 11:9.0064e-52 12:2.29734e-51 13:1.30952e-52 14:1.14509e-48 15:2.33791e-51 16:6.36074e-41 17:4.78319e-46 18:9.88362e-103 19:1.18759e-104 20:7.56195e-118 21:3.05295e-99 22:1.19914e-103 23:2.68201e-21 24:6.17375e-91 25:6.30612e-151 26:6.59257e-50 27:1.50964e-89 28:1.19137e-86 29:9.42612e-47 30:5.0609e-66 31:3.89768e-149 32:1.41179e-49 33:1.62746e-79 34:2.80803e-108 35:5.26342e-77 36:1.28883e-55 37:4.3514e-24 38:5.40903e-86 39:5.26603e-61 40:2.5533e-83 41:2.91799e-121 42:4.92685e-68 43:1.42043e-72 44:3.66844e-54 45:1.07013e-92 46:2.2805e-56 47:4.31802e-112 48:2.12206e-67 49:4.32273e-65 50:5.36831e-108 51:3.10334e-59 52:5.76347e-71 53:3.189e-74 54:1.16991e-15 55:2.31613e-120 56:4.17858e-69 57:3.11132e-70 58:6.68288e-27 59:1.72033e-105 60:7.81592e-63 61:7.91623e-64 62:9.43495e-63 63:1.05312e-74 64:9.53001e-123 65:2.04295e-66 66:5.71577e-30 67:5.90979e-108 68:8.76473e-54 69:2.51005e-73 70:2.08671e-81 71:9.14769e-38 72:5.51473e-31 73:2.33375e-44 74:1.11588e-46 75:1.80495e-39 76:3.66284e-49 77:1.52272e-44 78:4.28484e-71 79:8.19242e-23 80:7.09162e-57 81:1.31163e-58 82:7.40765e-44 83:1.63155e-65 84:6.85533e-61 85:1.67216e-60 86:3.10819e-77 87:7.99735e-26 88:2.20357e-81 89:2.67345e-53 90:7.94344e-34 91:2.97164e-83 92:5.35325e-70 93:4.00621e-67 94:9.56203e-61 95:8.90908e-50 96:2.06665e-60 97:4.78235e-53 98:2.39696e-50 99:1.73158e-52 100:4.63302e-32 101:1.96568e-84 102:9.10009e-69 103:1.6031e-73 104:8.72453e-44 105:3.37299e-88 106:5.02218e-44 107:1.70837e-107 108:6.30181e-110 109:6.10561e-89 110:6.96046e-35 111:2.86401e-101 112:2.9393e-31 113:4.69209e-129 114:2.34756e-56 115:9.01049e-68 116:3.00809e-54 ...
...
..
...
5906:9.52601e-72 5907:9.93085e-28 5908:1.0446e-76 5909:1.53848e-65 5910:6.02333e-52 5911:2.12289e-43 5912:7.00049e-71 5913:7.89907e-37 5914:8.86224e-60 5915:1.47167e-70
####################
cat seq_psam.dat
psam_001.xml
NM_000088.3 0.0301094
#########################
Could you please help me to understand these results ?
What is this matrix "aff_psam_001.xml" ?
How could I obtain more details on the affinity change and dynamics of binding site ?
Thank you in advance
Best Regards
Azadeh
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