DeepBind

Introduction

DeepBind Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

Official Website

How to use this tool

Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.

Each tool has at least 2 steps, but most of them have more:

  • The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
  • In the following steps, the user has the possibility to change the default tool parameters
  • And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server

Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.

Step 1 - Model

Databases

Database

Database Name Description Abbreviation
The protein family The deepbind model is presented by The protein family e.g. Homeodomain
RRM 190 RRM models D00084.001 D00086.001 D00086.002 D00086.003 D00087.001 D00088.001 D00089.001 D00091.001 D00092.001 D00093.001 D00095.001 D00096.001 D00097.001 D00100.001 D00101.001 D00102.001 D00102.002 D00102.003 D00102.004 D00104.001 D00105.001 D00106.001 D00107.001 D00108.001 D00110.001 D00110.002 D00111.001 D00111.002 D00112.001 D00113.001 D00114.001 D00114.002 D00114.003 D00114.004 D00114.005 D00119.001 D00122.001 D00122.002 D00122.003 D00123.001 D00123.002 D00125.001 D00127.001 D00130.001 D00131.001 D00132.001 D00134.001 D00135.001 D00136.002 D00137.001 D00138.001 D00138.002 D00139.001 D00140.001 D00141.001 D00142.001 D00145.001 D00147.001 D00148.001 D00148.002 D00149.001 D00149.002 D00149.003 D00150.001 D00151.001 D00152.001 D00153.001 D00156.001 D00157.001 D00157.002 D00158.001 D00159.001 D00160.001 D00161.001 D00167.001 D00168.001 D00168.002 D00168.003 D00169.001 D00169.002 D00169.003 D00169.004 D00169.005 D00169.006 D00171.001 D00172.001 D00173.001 D00174.001 D00175.001 D00176.001 D00177.001 D00179.001 D00180.001 D00181.001 D00182.001 D00184.001 D00185.001 D00186.001 D00187.001 D00189.001 D00190.001 D00191.001 D00192.001 D00193.001 D00194.001 D00195.001 D00196.001 D00197.001 D00198.001 D00199.001 D00200.001 D00201.001 D00202.001 D00203.001 D00204.001 D00205.001 D00207.001 D00208.001 D00209.001 D00210.001 D00212.001 D00213.001 D00215.001 D00216.001 D00217.001 D00218.001 D00219.001 D00220.001 D00221.001 D00222.001 D00225.001 D00226.001 D00227.001 D00228.001 D00229.001 D00230.001 D00231.001 D00232.001 D00233.001 D00234.001 D00236.001 D00237.001 D00238.001 D00239.001 D00240.001 D00241.001 D00242.001 D00243.001 D00244.001 D00245.001 D00246.001 D00247.001 D00248.001 D00249.001 D00250.001 D00251.001 D00252.001 D00253.001 D00255.001 D00256.001 D00257.001 D00259.001 D00260.001 D00261.001 D00262.001 D00263.001 D00264.001 D00265.001 D00266.001 D00267.001 D00268.001 D00269.001 D00270.001 D00271.001 D00272.001 D00274.001 D00274.002 D00275.001 D00277.001 D00278.001 D00279.001 D00280.001 D00281.001 D00282.001 D00283.001 D00284.001 D00285.001 D00286.001 D00287.001 D00288.001
Homeodomain 143 Homeodomain models D00066.001 D00289.002 D00290.003 D00291.002 D00292.001 D00294.001 D00295.002 D00301.003 D00302.003 D00303.002 D00313.002 D00314.001 D00315.003 D00316.003 D00332.003 D00333.004 D00334.002 D00335.003 D00336.001 D00337.001 D00338.002 D00339.002 D00340.003 D00341.003 D00342.003 D00343.003 D00364.002 D00365.003 D00366.003 D00367.003 D00368.007 D00377.001 D00385.002 D00386.001 D00413.003 D00414.003 D00415.003 D00416.005 D00425.002 D00426.003 D00427.003 D00428.002 D00431.002 D00439.003 D00440.003 D00441.003 D00442.003 D00443.001 D00444.001 D00447.002 D00448.002 D00449.002 D00450.003 D00451.002 D00452.001 D00453.002 D00454.003 D00455.001 D00456.001 D00457.003 D00458.003 D00459.003 D00460.003 D00461.003 D00462.002 D00463.003 D00464.001 D00465.003 D00466.003 D00467.002 D00468.003 D00469.003 D00481.003 D00482.003 D00483.001 D00484.003 D00485.004 D00491.003 D00493.003 D00494.002 D00495.003 D00496.002 D00497.002 D00498.002 D00499.001 D00508.004 D00509.001 D00510.003 D00511.002 D00512.001 D00513.002 D00514.003 D00515.002 D00518.002 D00522.002 D00524.002 D00525.002 D00526.001 D00543.005 D00544.005 D00545.002 D00546.003 D00547.003 D00548.002 D00549.002 D00550.002 D00551.002 D00567.002 D00568.001 D00569.002 D00578.002 D00579.002 D00580.005 D00581.002 D00582.001 D00583.002 D00584.001 D00585.003 D00602.008 D00604.004 D00605.003 D00606.002 D00612.001 D00613.002 D00620.003 D00621.003 D00632.001 D00633.001 D00634.001 D00689.003 D00690.003 D00691.001 D00698.001 D00699.001 D00701.001 D00702.001 D00705.003 D00706.001 D00707.004 D00708.001 D00786.001 D00791.001 D00806.003
C2H2 ZF 92 C2H2 ZF models D00002.001 D00017.001 D00020.001 D00024.001 D00024.004 D00025.001 D00026.001 D00028.001 D00028.002 D00047.001 D00048.001 D00049.001 D00050.001 D00051.001 D00052.001 D00052.002 D00052.003 D00058.001 D00058.004 D00075.001 D00078.001 D00079.001 D00080.001 D00081.001 D00082.001 D00305.003 D00328.003 D00328.018 D00351.001 D00351.006 D00351.009 D00353.005 D00354.002 D00355.002 D00419.003 D00420.004 D00421.003 D00422.003 D00434.003 D00435.003 D00488.003 D00489.002 D00490.003 D00527.003 D00600.001 D00600.004 D00601.003 D00630.003 D00631.002 D00636.003 D00650.005 D00650.007 D00651.003 D00652.003 D00652.004 D00653.003 D00710.002 D00710.007 D00711.003 D00713.003 D00714.003 D00714.004 D00715.002 D00716.004 D00717.003 D00718.002 D00719.002 D00720.002 D00721.002 D00722.002 D00723.003 D00723.006 D00724.003 D00725.004 D00726.003 D00728.002 D00730.002 D00731.003 D00732.005 D00733.003 D00734.003 D00735.002 D00742.002 D00753.001 D00774.001 D00781.003 D00799.001 D00809.002 D00825.001 D00827.001 D00828.002 D00829.002
bHLH 53 bHLH models D00019.001 D00027.001 D00027.003 D00040.001 D00040.003 D00065.001 D00293.003 D00297.002 D00300.003 D00306.003 D00307.001 D00308.003 D00309.002 D00310.002 D00311.003 D00312.002 D00322.002 D00350.002 D00350.005 D00388.003 D00429.003 D00430.003 D00432.003 D00433.003 D00474.003 D00516.002 D00519.002 D00520.002 D00521.003 D00523.003 D00530.003 D00531.003 D00532.003 D00542.005 D00561.001 D00562.006 D00563.002 D00659.002 D00671.003 D00672.001 D00673.001 D00684.005 D00686.002 D00687.001 D00688.002 D00700.001 D00700.006 D00746.004 D00784.004 D00785.001 D00815.001 D00818.003 D00823.002
Nuclear receptor 52 bHLH models D00003.001 D00014.001 D00021.001 D00021.005 D00030.001 D00030.004 D00031.001 D00036.001 D00059.001 D00060.001 D00067.001 D00067.004 D00068.001 D00069.001 D00071.001 D00071.003 D00073.001 D00296.006 D00372.003 D00373.003 D00374.003 D00375.003 D00376.003 D00445.003 D00446.005 D00446.009 D00552.002 D00552.006 D00553.003 D00554.003 D00555.002 D00556.003 D00557.002 D00558.002 D00607.006 D00608.002 D00609.002 D00610.003 D00611.001 D00622.003 D00625.001 D00626.005 D00626.009 D00627.002 D00628.002 D00629.006 D00692.002 D00693.002 D00703.002 D00704.001 D00773.001 D00790.001
bZIP 51 bZIP models D00001.001 D00001.004 D00022.001 D00022.002 D00029.001 D00046.001 D00054.001 D00055.001 D00055.004 D00165.001 D00298.003 D00299.003 D00304.003 D00317.003 D00317.009 D00318.001 D00318.004 D00319.003 D00320.001 D00324.003 D00325.003 D00326.002 D00327.002 D00331.006 D00437.004 D00438.003 D00486.002 D00487.003 D00500.002 D00501.003 D00501.004 D00502.002 D00503.004 D00503.014 D00535.003 D00535.004 D00538.001 D00560.003 D00680.001 D00709.002 D00737.001 D00738.002 D00739.001 D00740.002 D00741.001 D00758.001 D00759.001 D00760.003 D00775.001 D00776.005 D00777.002
Forkhead 33 Forkhead models D00004.001 D00005.001 D00006.001 D00007.001 D00008.001 D00009.001 D00023.001 D00061.001 D00062.001 D00062.004 D00390.002 D00391.003 D00392.002 D00393.003 D00394.003 D00395.002 D00396.003 D00397.003 D00398.001 D00399.002 D00400.003 D00401.003 D00402.001 D00403.001 D00404.002 D00405.003 D00406.002 D00407.003 D00408.003 D00761.001 D00762.001 D00763.001 D00764.001
Ets 31 Ets D00356.005 D00356.010 D00357.002 D00358.003 D00359.004 D00360.004 D00360.007 D00361.001 D00362.002 D00363.003 D00363.004 D00370.003 D00371.003 D00378.007 D00378.009 D00379.001 D00380.002 D00381.003 D00382.003 D00383.002 D00384.002 D00387.001 D00389.005 D00409.003 D00409.004 D00654.003 D00655.002 D00655.006 D00656.001 D00657.003 D00658.003
KH 24 KH models D00085.001 D00090.001 D00094.001 D00098.001 D00099.001 D00103.001 D00109.001 D00116.001 D00126.001 D00129.001 D00143.001 D00146.001 D00170.001 D00178.001 D00183.001 D00188.001 D00206.001 D00211.001 D00223.001 D00224.001 D00235.001 D00254.001 D00258.001 D00273.001
Sox 24 Sox D00016.001 D00037.001 D00037.003 D00038.001 D00038.003 D00039.001 D00492.003 D00637.003 D00638.003 D00639.003 D00640.003 D00641.002 D00642.003 D00644.003 D00645.006 D00646.002 D00647.002 D00648.004 D00649.002 D00661.003 D00674.003 D00675.001 D00819.002 D00822.001
Homeodomain,POU 18 Homeodomain,POU D00015.001 D00034.001 D00070.001 D00586.004 D00587.002 D00588.002 D00589.001 D00589.005 D00590.001 D00591.002 D00592.003 D00593.003 D00594.002 D00595.001 D00596.005 D00597.001 D00599.006 D00795.001
T-box 17 T-box D00018.001 D00041.001 D00042.001 D00043.001 D00044.001 D00077.001 D00369.003 D00662.003 D00663.002 D00664.002 D00665.002 D00666.002 D00667.001 D00668.003 D00669.002 D00670.002 D00697.002

Step 2 - Sequence

Sequence Input Window

DNA/RNA sequences

Sequence File Upload

A file containing DNA/RNA sequences.

Step 3 - Submission

Job title

It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.

Email Notification

Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.

Email Address

If email notification is requested, then a valid Internet email address in the form test@altoromutual.com must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).

References

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning.
(2015 July 27) Nature biotechnology 33 (8) :831-838
PMID: 26213851