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@@ -24,43 +24,48 @@ EXAMPLE
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  To generate predictions with DeepBind, you need two things:
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  1) a list of model IDs, and
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- 2) a list of DNA/RNA sequences.
 
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  The file example.ids contains 4 example model IDs, one
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  on each line, reproduced here:
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- D00210.001 # RBFOX1 (RNAcompete)
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- D00120.001 # MBNL1 (RNAcompete)
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- D00410.003 # GATA3 (SELEX)
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- D00328.003 # CTCF (SELEX)
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  The file example.seq contains 4 example sequences, which
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  were chosen such that the nth sequence scores highly for
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  the nth model. The file example.seq is reproduced here:
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- AGGUAAUAAUUUGCAUGAAAUAACUUGGAGAGGAUAGC
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- AGACAGAGCUUCCAUCAGCGCUAGCAGCAGAGACCAUU
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- GAGGTTACGCGGCAAGATAA
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- TACCACTAGGGGGCGCCACC
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  To generate 16 predictions (4 models, 4 sequences), run
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  the deepbind executable as follows:
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  % deepbind example.ids < example.seq
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- D00210.001 D00120.001 D00410.003 D00328.003
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- 7.451420 -0.166146 -0.408751 -0.026180
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- -0.155398 4.113817 0.516956 -0.248167
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- -0.140683 0.181295 5.885349 -0.026180
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- -0.174985 -0.152521 -0.379695 17.682623
 
 
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  To see details of each ID, use the --dump-info flag:
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  % deepbind --dump-info example.ids
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- ID Protein Type Species Family Class Experiment ...
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- D00210.001 RBFOX1 RBP Homo sapiens RRM RNAcompete ...
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- D00120.001 MBNL1 RBP Homo sapiens Znf RNAcompete ...
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- D00410.003 GATA3 TF Homo sapiens GATA SELEX ...
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- D00328.003 CTCF TF Homo sapiens C2H2 ZF SELEX ...
 
 
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  To generate predictions with DeepBind, you need two things:
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  1) a list of model IDs, and
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+ 2)
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+ 3) a list of DNA/RNA sequences.
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  The file example.ids contains 4 example model IDs, one
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  on each line, reproduced here:
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+ * D00210.001 # RBFOX1 (RNAcompete)
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+ * D00120.001 # MBNL1 (RNAcompete)
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+ * D00410.003 # GATA3 (SELEX)
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+ * D00328.003 # CTCF (SELEX)
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  The file example.seq contains 4 example sequences, which
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  were chosen such that the nth sequence scores highly for
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  the nth model. The file example.seq is reproduced here:
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+ * AGGUAAUAAUUUGCAUGAAAUAACUUGGAGAGGAUAGC
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+ * AGACAGAGCUUCCAUCAGCGCUAGCAGCAGAGACCAUU
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+ * GAGGTTACGCGGCAAGATAA
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+ * TACCACTAGGGGGCGCCACC
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  To generate 16 predictions (4 models, 4 sequences), run
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  the deepbind executable as follows:
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  % deepbind example.ids < example.seq
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+
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+ |D00210.001| D00120.001| D00410.003| D00328.003|
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+ | :----:| :----: | :----: |:----: |
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+ | 7.451420 | -0.166146 | -0.408751| -0.026180|
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+ | -0.155398 | 4.113817 | 0.516956| -0.248167|
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+ | -0.140683 | 0.181295 | 5.885349| -0.026180|
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+ | -0.174985 | -0.152521 | -0.379695| 17.682623|
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  To see details of each ID, use the --dump-info flag:
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  % deepbind --dump-info example.ids
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+
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+ |ID | Protein | Type | Species | Family | Class Experiment |
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+ | :----:| :----: | :----: |:----: | :----: | :----: |
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+ | D00210.001 |RBFOX1 |RBP |Homo sapiens |RRM |RNAcompete |
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+ | D00120.001 |MBNL1 |RBP |Homo sapiens |Znf |RNAcompete |
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+ | D00410.003 |GATA3 |TF |Homo sapiens |GATA |SELEX |
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+ | D00328.003 |CTCF |TF |Homo sapiens |C2H2 ZF |SELEX |
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