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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| + | MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE |
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| − | LLHHHHHHHHHHHHLLLLHHHHHHHLLLLLLLELLLLLLL |
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| + | LLHHHHHHHHHHHHLLLLHHHHHHHLLLLLLLELLLLLLLLHLLLLLLLLLLLLLLLLHHHHHHHHLLLLLLELLLLEEEEELLLLLEELLLLLLLLLHH |
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| + | KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER |
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| − | QQQQFSSLDDKPQFPGASAEFIDKLEFIQPNVISGIPIYR |
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| + | HHHHHHHHHHHHHLHLHHEEELLLLLEEEEEEELLLLLLLLELLLLELLLLLEEEEEELLLLEEEELLLLHHHHHHHHHLLHLLLLLLLLLLLELLLLLL |
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| − | LHLLLLLLLLLLLLLLLLHHHHHHHHLLLLLLELLLLEEE |
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| + | HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG |
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| − | VMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILY |
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| + | EEEEELLLHHHHLHHHHHHHHHHHHLLLLEEEEEEELLLLLLLLLLLLLLEEEEELLLLEEEEEELLLEEELLLLLLLELLLLEELLLLLEEEEEEEELL |
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| − | EELLLLLEELLLLLLLLLHHHHHHHHHHHHHHHLHLHHEE |
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| + | NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK |
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| − | ESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYRE |
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| + | LLEEEEELLLHHHHHHHHHLLLLEEEEHEEEEELLLLLLLLLLHLLLLLLLLLLLLLLLLHHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHHHHHHHHLL |
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| − | ELLLLLEEEEEEELLLLLLLLELLLLELLLLLEEEEEELL |
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| + | PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK |
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| − | AGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER |
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| + | LLLLLLEEELHHHHHLHHHHHHHHHHHHHHHHHHLLLLLLLLLLL |
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| − | LLEEEELLLLHHHHHHHHHLLHLLLLLLLLLLLELLLLLL |
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| − | |||
| − | HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGA |
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| − | EEEEELLLHHHHLHHHHHHHHHHHHLLLLEEEEEEELLLL |
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| − | |||
| − | ASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYR |
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| − | LLLLLLLLLLEEEEELLLLEEEEEELLLEEELLLLLLLEL |
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| − | |||
| − | GDGIAARGPGYGIMSIRVDGNDVFAVYNATKEARRRAVAE |
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| − | LLLEELLLLLEEEEEEEELLLLEEEEELLLHHHHHHHHHL |
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| − | |||
| − | NQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHP |
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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 14:45, 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:
MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE LLHHHHHHHHHHHHLLLLHHHHHHHLLLLLLLELLLLLLLLHLLLLLLLLLLLLLLLLHHHHHHHHLLLLLLELLLLEEEEELLLLLEELLLLLLLLLHH KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER HHHHHHHHHHHHHLHLHHEEELLLLLEEEEEEELLLLLLLLELLLLELLLLLEEEEEELLLLEEEELLLLHHHHHHHHHLLHLLLLLLLLLLLELLLLLL HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG EEEEELLLHHHHLHHHHHHHHHHHHLLLLEEEEEEELLLLLLLLLLLLLLEEEEELLLLEEEEEELLLEEELLLLLLLELLLLEELLLLLEEEEEEEELL NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK LLEEEEELLLHHHHHHHHHLLLLEEEEHEEEEELLLLLLLLLLHLLLLLLLLLLLLLLLLHHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHHHHHHHHLL PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK LLLLLLEEELHHHHHLHHHHHHHHHHHHHHHHHHLLLLLLLLLLL
