Difference between revisions of "Task 3: odba human Sequence-based predictions"
From Bioinformatikpedia
(→secondary structure) |
(→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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| + | <table border=1> |
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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> |
||
| + | <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> |
||
| + | <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> |
||
| + | <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> |
||
| + | <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> |
||
| + | <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> |
||
| + | <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> |
||
| + | <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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| + | <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> |
||
| + | <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> |
||
| + | <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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| + | <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> |
||
| + | <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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| + | <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> |
||
| + | <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> |
||
| + | <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> |
||
| + | <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> |
||
| + | <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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| + | <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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| + | <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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| + | <td>D</td><td>H</td><td>F</td><td>D</td><td>K</td><td></td></table> |
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= Disorder = |
= Disorder = |
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Revision as of 14:36, 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:
| M | A | V | A | I | A | A | A | R | V | W | R | L | N | R | G | L | S | Q | A | A | L | L | L | L | R | Q | P | G | A | R | G | L | A | R | S | H | P | P | R | |
| L | L | H | H | H | H | H | H | H | H | H | H | H | H | L | L | L | L | H | H | H | H | H | H | H | L | L | L | L | L | L | L | E | L | L | L | L | L | L | L | |
| Q | Q | Q | Q | F | S | S | L | D | D | K | P | Q | F | P | G | A | S | A | E | F | I | D | K | L | E | F | I | Q | P | N | V | I | S | G | I | P | I | Y | R | |
| L | H | L | L | L | L | L | L | L | L | L | L | L | L | L | L | L | L | H | H | H | H | H | H | H | H | L | L | L | L | L | L | E | L | L | L | L | E | E | E | |
| V | M | D | R | Q | G | Q | I | I | N | P | S | E | D | P | H | L | P | K | E | K | V | L | K | L | Y | K | S | M | T | L | L | N | T | M | D | R | I | L | Y | |
| E | E | L | L | L | L | L | E | E | L | L | L | L | L | L | L | L | L | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | L | H | L | H | H | E | E | |
| E | S | Q | R | Q | G | R | I | S | F | Y | M | T | N | Y | G | E | E | G | T | H | V | G | S | A | A | A | L | D | N | T | D | L | V | F | G | Q | Y | R | E | |
| E | L | L | L | L | L | E | E | E | E | E | E | E | L | L | L | L | L | L | L | L | E | L | L | L | L | E | L | L | L | L | L | E | E | E | E | E | E | L | L | |
| A | G | V | L | M | Y | R | D | Y | P | L | E | L | F | M | A | Q | C | Y | G | N | I | S | D | L | G | K | G | R | Q | M | P | V | H | Y | G | C | K | E | R | |
| L | L | E | E | E | E | L | L | L | L | H | H | H | H | H | H | H | H | H | L | L | H | L | L | L | L | L | L | L | L | L | L | L | E | L | L | L | L | L | L | |
| H | F | V | T | I | S | S | P | L | A | T | Q | I | P | Q | A | V | G | A | A | Y | A | A | K | R | A | N | A | N | R | V | V | I | C | Y | F | G | E | G | A | |
| E | E | E | E | E | L | L | L | H | H | H | H | L | H | H | H | H | H | H | H | H | H | H | H | H | L | L | L | L | E | E | E | E | E | E | E | L | L | L | L | |
| A | S | E | G | D | A | H | A | G | F | N | F | A | A | T | L | E | C | P | I | I | F | F | C | R | N | N | G | Y | A | I | S | T | P | T | S | E | Q | Y | R | |
| L | L | L | L | L | L | L | L | L | L | E | E | E | E | E | L | L | L | L | E | E | E | E | E | E | L | L | L | E | E | E | L | L | L | L | L | L | L | E | L | |
| G | D | G | I | A | A | R | G | P | G | Y | G | I | M | S | I | R | V | D | G | N | D | V | F | A | V | Y | N | A | T | K | E | A | R | R | R | A | V | A | E | |
| L | L | L | E | E | L | L | L | L | L | E | E | E | E | E | E | E | E | L | L | L | L | E | E | E | E | E | L | L | L | H | H | H | H | H | H | H | H | H | L | |
| N | Q | P | F | L | I | E | A | M | T | Y | R | I | G | H | H | S | T | S | D | D | S | S | A | Y | R | S | V | D | E | V | N | Y | W | D | K | Q | D | H | P | |
| L | L | L | E | E | E | E | H | E | E | E | E | E | L | L | L | L | L | L | L | L | L | L | H | L | L | L | L | L | L | L | L | L | L | L | L | L | L | L | L | |
| I | S | R | L | R | H | Y | L | L | S | Q | G | W | W | D | E | E | Q | E | K | A | W | R | K | Q | S | R | R | K | V | M | E | A | F | E | Q | A | E | R | K | |
| H | H | H | H | H | H | H | H | H | L | L | L | L | L | L | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | L | L | |
| P | K | P | N | P | N | L | L | F | S | D | V | Y | Q | E | M | P | A | Q | L | R | K | Q | Q | E | S | L | A | R | H | L | Q | T | Y | G | E | H | Y | P | L | |
| L | L | L | L | L | L | E | E | E | L | H | H | H | H | H | L | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | H | L | L | L | L | L | L | |
| D | H | F | D | K |
