Difference between revisions of "Task 3: odba human Sequence-based predictions"
From Bioinformatikpedia
(→reprof) |
(→reprof) |
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reprof then calculates the secondary structure prediction and provides an output file "seq.fasta.reprof" |
reprof then calculates the secondary structure prediction and provides an output file "seq.fasta.reprof" |
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Result: |
Result: |
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| + | MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPR |
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| − | <table border=1> |
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| + | LLHHHHHHHHHHHHLLLLHHHHHHHLLLLLLLELLLLLLL |
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| − | <tr><td> |
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| + | |||
| − | <td>M</td><td>A</td><td>V</td><td>A</td><td>I</td><td>A</td><td>A</td><td>A</td><td>R</td><td>V</td><td>W</td><td>R</td><td>L</td><td>N</td><td>R</td><td>G</td><td>L</td><td>S</td><td>Q</td><td>A</td><td>A</td><td>L</td><td>L</td><td>L</td><td>L</td><td>R</td><td>Q</td><td>P</td><td>G</td><td>A</td><td>R</td><td>G</td><td>L</td><td>A</td><td>R</td><td>S</td><td>H</td><td>P</td><td>P</td><td>R</td></tr><tr> |
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| + | QQQQFSSLDDKPQFPGASAEFIDKLEFIQPNVISGIPIYR |
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| − | <td>L</td><td>L</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>L</td><td>L</td><td>L</td><td>L</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td></tr><tr> |
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| + | LHLLLLLLLLLLLLLLLLHHHHHHHHLLLLLLELLLLEEE |
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| − | <td>Q</td><td>Q</td><td>Q</td><td>Q</td><td>F</td><td>S</td><td>S</td><td>L</td><td>D</td><td>D</td><td>K</td><td>P</td><td>Q</td><td>F</td><td>P</td><td>G</td><td>A</td><td>S</td><td>A</td><td>E</td><td>F</td><td>I</td><td>D</td><td>K</td><td>L</td><td>E</td><td>F</td><td>I</td><td>Q</td><td>P</td><td>N</td><td>V</td><td>I</td><td>S</td><td>G</td><td>I</td><td>P</td><td>I</td><td>Y</td><td>R</td></tr><tr> |
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| + | |||
| − | <td>L</td><td>H</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>E</td></tr><tr> |
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| + | VMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILY |
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| − | <td>V</td><td>M</td><td>D</td><td>R</td><td>Q</td><td>G</td><td>Q</td><td>I</td><td>I</td><td>N</td><td>P</td><td>S</td><td>E</td><td>D</td><td>P</td><td>H</td><td>L</td><td>P</td><td>K</td><td>E</td><td>K</td><td>V</td><td>L</td><td>K</td><td>L</td><td>Y</td><td>K</td><td>S</td><td>M</td><td>T</td><td>L</td><td>L</td><td>N</td><td>T</td><td>M</td><td>D</td><td>R</td><td>I</td><td>L</td><td>Y</td></tr><tr> |
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| + | EELLLLLEELLLLLLLLLHHHHHHHHHHHHHHHLHLHHEE |
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| − | <td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>L</td><td>H</td><td>L</td><td>H</td><td>H</td><td>E</td><td>E</td></tr><tr> |
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| + | |||
| − | <td>E</td><td>S</td><td>Q</td><td>R</td><td>Q</td><td>G</td><td>R</td><td>I</td><td>S</td><td>F</td><td>Y</td><td>M</td><td>T</td><td>N</td><td>Y</td><td>G</td><td>E</td><td>E</td><td>G</td><td>T</td><td>H</td><td>V</td><td>G</td><td>S</td><td>A</td><td>A</td><td>A</td><td>L</td><td>D</td><td>N</td><td>T</td><td>D</td><td>L</td><td>V</td><td>F</td><td>G</td><td>Q</td><td>Y</td><td>R</td><td>E</td></tr><tr> |
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| + | ESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYRE |
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| − | <td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>L</td><td>L</td></tr><tr> |
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| + | ELLLLLEEEEEEELLLLLLLLELLLLELLLLLEEEEEELL |
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| − | <td>A</td><td>G</td><td>V</td><td>L</td><td>M</td><td>Y</td><td>R</td><td>D</td><td>Y</td><td>P</td><td>L</td><td>E</td><td>L</td><td>F</td><td>M</td><td>A</td><td>Q</td><td>C</td><td>Y</td><td>G</td><td>N</td><td>I</td><td>S</td><td>D</td><td>L</td><td>G</td><td>K</td><td>G</td><td>R</td><td>Q</td><td>M</td><td>P</td><td>V</td><td>H</td><td>Y</td><td>G</td><td>C</td><td>K</td><td>E</td><td>R</td></tr><tr> |
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| + | |||
| − | <td>L</td><td>L</td><td>E</td><td>E</td><td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>L</td><td>L</td><td>H</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td></tr><tr> |
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| + | AGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER |
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| − | <td>H</td><td>F</td><td>V</td><td>T</td><td>I</td><td>S</td><td>S</td><td>P</td><td>L</td><td>A</td><td>T</td><td>Q</td><td>I</td><td>P</td><td>Q</td><td>A</td><td>V</td><td>G</td><td>A</td><td>A</td><td>Y</td><td>A</td><td>A</td><td>K</td><td>R</td><td>A</td><td>N</td><td>A</td><td>N</td><td>R</td><td>V</td><td>V</td><td>I</td><td>C</td><td>Y</td><td>F</td><td>G</td><td>E</td><td>G</td><td>A</td></tr><tr> |
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| + | LLEEEELLLLHHHHHHHHHLLHLLLLLLLLLLLELLLLLL |
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| − | <td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>H</td><td>H</td><td>H</td><td>H</td><td>L</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td></tr><tr> |
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| + | |||
| − | <td>A</td><td>S</td><td>E</td><td>G</td><td>D</td><td>A</td><td>H</td><td>A</td><td>G</td><td>F</td><td>N</td><td>F</td><td>A</td><td>A</td><td>T</td><td>L</td><td>E</td><td>C</td><td>P</td><td>I</td><td>I</td><td>F</td><td>F</td><td>C</td><td>R</td><td>N</td><td>N</td><td>G</td><td>Y</td><td>A</td><td>I</td><td>S</td><td>T</td><td>P</td><td>T</td><td>S</td><td>E</td><td>Q</td><td>Y</td><td>R</td></tr><tr> |
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| + | HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGA |
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| − | <td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>L</td></tr><tr> |
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| + | EEEEELLLHHHHLHHHHHHHHHHHHLLLLEEEEEEELLLL |
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| − | <td>G</td><td>D</td><td>G</td><td>I</td><td>A</td><td>A</td><td>R</td><td>G</td><td>P</td><td>G</td><td>Y</td><td>G</td><td>I</td><td>M</td><td>S</td><td>I</td><td>R</td><td>V</td><td>D</td><td>G</td><td>N</td><td>D</td><td>V</td><td>F</td><td>A</td><td>V</td><td>Y</td><td>N</td><td>A</td><td>T</td><td>K</td><td>E</td><td>A</td><td>R</td><td>R</td><td>R</td><td>A</td><td>V</td><td>A</td><td>E</td></tr><tr> |
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| + | |||
| − | <td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>L</td></tr><tr> |
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| + | ASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYR |
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| − | <td>N</td><td>Q</td><td>P</td><td>F</td><td>L</td><td>I</td><td>E</td><td>A</td><td>M</td><td>T</td><td>Y</td><td>R</td><td>I</td><td>G</td><td>H</td><td>H</td><td>S</td><td>T</td><td>S</td><td>D</td><td>D</td><td>S</td><td>S</td><td>A</td><td>Y</td><td>R</td><td>S</td><td>V</td><td>D</td><td>E</td><td>V</td><td>N</td><td>Y</td><td>W</td><td>D</td><td>K</td><td>Q</td><td>D</td><td>H</td><td>P</td></tr><tr> |
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| + | LLLLLLLLLLEEEEELLLLEEEEEELLLEEELLLLLLLEL |
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| − | <td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>E</td><td>E</td><td>H</td><td>E</td><td>E</td><td>E</td><td>E</td><td>E</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>H</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td></tr><tr> |
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| + | |||
| − | <td>I</td><td>S</td><td>R</td><td>L</td><td>R</td><td>H</td><td>Y</td><td>L</td><td>L</td><td>S</td><td>Q</td><td>G</td><td>W</td><td>W</td><td>D</td><td>E</td><td>E</td><td>Q</td><td>E</td><td>K</td><td>A</td><td>W</td><td>R</td><td>K</td><td>Q</td><td>S</td><td>R</td><td>R</td><td>K</td><td>V</td><td>M</td><td>E</td><td>A</td><td>F</td><td>E</td><td>Q</td><td>A</td><td>E</td><td>R</td><td>K</td></tr><tr> |
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| + | GDGIAARGPGYGIMSIRVDGNDVFAVYNATKEARRRAVAE |
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| − | <td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>L</td><td>L</td></tr><tr> |
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| + | LLLEELLLLLEEEEEEEELLLLEEEEELLLHHHHHHHHHL |
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| − | <td>P</td><td>K</td><td>P</td><td>N</td><td>P</td><td>N</td><td>L</td><td>L</td><td>F</td><td>S</td><td>D</td><td>V</td><td>Y</td><td>Q</td><td>E</td><td>M</td><td>P</td><td>A</td><td>Q</td><td>L</td><td>R</td><td>K</td><td>Q</td><td>Q</td><td>E</td><td>S</td><td>L</td><td>A</td><td>R</td><td>H</td><td>L</td><td>Q</td><td>T</td><td>Y</td><td>G</td><td>E</td><td>H</td><td>Y</td><td>P</td><td>L</td></tr><tr> |
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| + | |||
| − | <td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>E</td><td>E</td><td>E</td><td>L</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>L</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>H</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td><td>L</td></tr><tr> |
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| + | NQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHP |
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| − | <td>D</td><td>H</td><td>F</td><td>D</td><td>K</td><td></td></table> |
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| + | LLLEEEEHEEEEELLLLLLLLLLHLLLLLLLLLLLLLLLL |
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| + | |||
| + | ISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK |
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| + | HHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHHHHHHHHLL |
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| + | |||
| + | PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPL |
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| + | LLLLLLEEELHHHHHLHHHHHHHHHHHHHHHHHHLLLLLL |
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| + | |||
| + | DHFDK |
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| + | LLLLL |
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= Disorder = |
= Disorder = |
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Revision as of 14:43, 12 May 2012
Contents
secondary structure
To predict secondary structure we use the following tools and compare the results:
-reprof -psipred -DSSP_Server
reprof
to run reprof from the command line the following command is used:
reprof -i seq.fasta
reprof then calculates the secondary structure prediction and provides an output file "seq.fasta.reprof" Result:
MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPR LLHHHHHHHHHHHHLLLLHHHHHHHLLLLLLLELLLLLLL QQQQFSSLDDKPQFPGASAEFIDKLEFIQPNVISGIPIYR LHLLLLLLLLLLLLLLLLHHHHHHHHLLLLLLELLLLEEE VMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILY EELLLLLEELLLLLLLLLHHHHHHHHHHHHHHHLHLHHEE ESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYRE ELLLLLEEEEEEELLLLLLLLELLLLELLLLLEEEEEELL AGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER LLEEEELLLLHHHHHHHHHLLHLLLLLLLLLLLELLLLLL HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGA EEEEELLLHHHHLHHHHHHHHHHHHLLLLEEEEEEELLLL ASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYR LLLLLLLLLLEEEEELLLLEEEEEELLLEEELLLLLLLEL GDGIAARGPGYGIMSIRVDGNDVFAVYNATKEARRRAVAE LLLEELLLLLEEEEEEEELLLLEEEEELLLHHHHHHHHHL NQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHP LLLEEEEHEEEEELLLLLLLLLLHLLLLLLLLLLLLLLLL ISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK HHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHHHHHHHHLL
PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPL LLLLLLEEELHHHHHLHHHHHHHHHHHHHHHHHHLLLLLL DHFDK LLLLL
