| --- |
| license: openrail |
| --- |
| DEEPBIND v0.11 |
| -------------- |
|
|
| The deepbind command-line executable can be used to score DNA/RNA sequences |
| according to any RBP/TF model listed in the DeepBind web repository: |
|
|
| http://tools.genes.toronto.edu/deepbind |
|
|
| For each input sequence, the deepbind executable scores each subsequence |
| of a pre-determined length (e.g. 20) and returns only the maximum or the |
| average over these per-position scores. |
|
|
| Larger scores indicated stronger binding. The scores themselves are on an |
| arbitrary scale, and vary from model to model due to variation in the |
| quality of training data for different proteins. |
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|
| EXAMPLE |
| ------- |
|
|
| To generate predictions with DeepBind, you need two things: |
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|
| 1) a list of model IDs, and |
| 2) |
| 3) a list of DNA/RNA sequences. |
|
|
| The file example.ids contains 4 example model IDs, one |
| on each line, reproduced here: |
|
|
| * D00210.001 # RBFOX1 (RNAcompete) |
| * D00120.001 # MBNL1 (RNAcompete) |
| * D00410.003 # GATA3 (SELEX) |
| * D00328.003 # CTCF (SELEX) |
|
|
| The file example.seq contains 4 example sequences, which |
| were chosen such that the nth sequence scores highly for |
| the nth model. The file example.seq is reproduced here: |
|
|
| * AGGUAAUAAUUUGCAUGAAAUAACUUGGAGAGGAUAGC |
| * AGACAGAGCUUCCAUCAGCGCUAGCAGCAGAGACCAUU |
| * GAGGTTACGCGGCAAGATAA |
| * TACCACTAGGGGGCGCCACC |
|
|
| To generate 16 predictions (4 models, 4 sequences), run |
| the deepbind executable as follows: |
|
|
| % deepbind example.ids < example.seq |
|
|
| |D00210.001| D00120.001| D00410.003| D00328.003| |
| | :----:| :----: | :----: |:----: | |
| | 7.451420 | -0.166146 | -0.408751| -0.026180| |
| | -0.155398 | 4.113817 | 0.516956| -0.248167| |
| | -0.140683 | 0.181295 | 5.885349| -0.026180| |
| | -0.174985 | -0.152521 | -0.379695| 17.682623| |
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| To see details of each ID, use the --dump-info flag: |
|
|
| % deepbind --dump-info example.ids |
| |
| |ID | Protein | Type | Species | Family | Class Experiment | |
| | :----:| :----: | :----: |:----: | :----: | :----: | |
| | D00210.001 |RBFOX1 |RBP |Homo sapiens |RRM |RNAcompete | |
| | D00120.001 |MBNL1 |RBP |Homo sapiens |Znf |RNAcompete | |
| | D00410.003 |GATA3 |TF |Homo sapiens |GATA |SELEX | |
| | D00328.003 |CTCF |TF |Homo sapiens |C2H2 ZF |SELEX | |
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| CHANGES v0.1 -> v0.11 |
| --------------------- |
|
|
| - Fixed bug where last position in input sequence was |
| not evaluated for a score; suggested by Irene Kaplow. |
|
|
| - Added --window-size and --average flags based on feedback. |
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