Difference between revisions of "Task 3: odba human Sequence-based predictions"
From Bioinformatikpedia
(→reprof) |
(→reprof) |
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| Line 9: | Line 9: | ||
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: (H = Helix, E = Extended/Sheet, L = Loop) |
Result: (H = Helix, E = Extended/Sheet, L = Loop) |
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| + | obda_human |
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Reliability( 0-9 (most reliable) ) |
Reliability( 0-9 (most reliable) ) |
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sec-structure |
sec-structure |
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| Line 31: | Line 32: | ||
LLLLLLEEELHHHHHLHHHHHHHHHHHHHHHHHHLLLLLLLLLLL |
LLLLLLEEELHHHHHLHHHHHHHHHHHHHHHHHHLLLLLLLLLLL |
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PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK |
PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK |
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| + | |||
| + | P10775 |
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| + | Reliability( 0-9 (most reliable) ) |
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| + | sec-structure |
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| + | AA-sequence |
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| + | |||
| + | 9721000003610177776776314314516778775677778877514877115421004336431001011566864102210024543110024337 |
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| + | LLLLELHHLLLLLHHHHHHHHHHHLLEEEELLLLLLHHHHHHHHHHHHLLLLHHHHHHHHLLLLLLLHEEEHLLLLLLLLEEEEELLLLLLLLHLLLLLL |
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| + | MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRTNELGDAGVHLVLQGLQSPTCKIQKLSLQNCSLTEAGCGVL |
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| + | |||
| + | 0133000013330258887661566556631578202223423334201324622688888888877652057775225666664004000153444411 |
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| + | HHHHLHLHHHHHHLLLLLLLLHHHHHHHHHLLLLLHLLHHHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHLLLLLLHHHHHHHHHLLLLLLHHHHHHHHH |
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| + | PSTLRSLPTLRELHLSDNPLGDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELTVSNNDIGEAGARVLGQGLADSACQLETLR |
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| + | |||
| + | 1047778532245655530000101103476775603366543044581121001011000456101257888875566677776613656705677777 |
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| + | HLLLLLLLLLHHHHHHHHHLHLLHHHLLLLLLLLLHHHHHHHLLLLLLLHHHHLHHEEEHLLLLLHHHHHHHHHHHHHHHHHHHHHHLLLLLLHHHHHHH |
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| + | LENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIAELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLLC |
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| + | |||
| + | 7631777612221231100357767777776410311433210357677236888888842788636677614532246313688888875112001025 |
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| + | HHHLLLLLLHHHHHHHHLHHHHHHHHHHHHHHHLLHHHHHHHLLLLLLLLHHHHHHHHHHLLLLLEEEEEEELLLLLLLLLHHHHHHHHHHHLLHHHHLL |
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| + | ESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQALSQPGTTLRVLCLGDCEVTNSGCSSLASLLLANRSLRELDL |
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| + | |||
| + | 65766771365554034675421654433056661778999988407888851138 |
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| + | LLLLLLLHHHHHHHLLLLLLLLHHHHHHHLLLLLLHHHHHHHHHHHLLLLLLLELL |
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| + | SNNCVGDPGVLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS |
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= Disorder = |
= Disorder = |
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Revision as of 14:57, 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: (H = Helix, E = Extended/Sheet, L = Loop)
obda_human Reliability( 0-9 (most reliable) ) sec-structure AA-sequence 9221124455554036207776653067862000247852012212357787787762666544200476501154066765467703167878778656 LLHHHHHHHHHHHHLLLLHHHHHHHLLLLLLLELLLLLLLLHLLLLLLLLLLLLLLLLHHHHHHHHLLLLLLELLLLEEEEELLLLLEELLLLLLLLLHH MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKE 7776655320100000301100557547888740466664011100046751342012001024530573233245541430113666535300255543 HHHHHHHHHHHHHLHLHHEEELLLLLEEEEEEELLLLLLLLELLLLELLLLLEEEEEELLLLEEEELLLLHHHHHHHHHLLHLLLLLLLLLLLELLLLLL KVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHYGCKER 2565305212002477767777653177627888842564565652123003342344178887067503105676210256402047640478887567 EEEEELLLHHHHLHHHHHHHHHHHHLLLLEEEEEEELLLLLLLLLLLLLLEEEEELLLLEEEEEELLLEEELLLLLLLELLLLEELLLLLEEEEEEEELL HFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG 7234432321577765553267212200001212125776522000114312346677733555545324788866888888643278889998876138 LLEEEEELLLHHHHHHHHHLLLLEEEEHEEEEELLLLLLLLLLHLLLLLLLLLLLLLLLLHHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHHHHHHHHLL NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERK 898975011024431728777888989998887256688886799 LLLLLLEEELHHHHHLHHHHHHHHHHHHHHHHHHLLLLLLLLLLL PKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYGEHYPLDHFDK
P10775 Reliability( 0-9 (most reliable) ) sec-structure AA-sequence
9721000003610177776776314314516778775677778877514877115421004336431001011566864102210024543110024337 LLLLELHHLLLLLHHHHHHHHHHHLLEEEELLLLLLHHHHHHHHHHHHLLLLHHHHHHHHLLLLLLLHEEEHLLLLLLLLEEEEELLLLLLLLHLLLLLL MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRTNELGDAGVHLVLQGLQSPTCKIQKLSLQNCSLTEAGCGVL 0133000013330258887661566556631578202223423334201324622688888888877652057775225666664004000153444411 HHHHLHLHHHHHHLLLLLLLLHHHHHHHHHLLLLLHLLHHHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHLLLLLLHHHHHHHHHLLLLLLHHHHHHHHH PSTLRSLPTLRELHLSDNPLGDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELTVSNNDIGEAGARVLGQGLADSACQLETLR 1047778532245655530000101103476775603366543044581121001011000456101257888875566677776613656705677777 HLLLLLLLLLHHHHHHHHHLHLLHHHLLLLLLLLLHHHHHHHLLLLLLLHHHHLHHEEEHLLLLLHHHHHHHHHHHHHHHHHHHHHHLLLLLLHHHHHHH LENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIAELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLLC 7631777612221231100357767777776410311433210357677236888888842788636677614532246313688888875112001025 HHHLLLLLLHHHHHHHHLHHHHHHHHHHHHHHHLLHHHHHHHLLLLLLLLHHHHHHHHHHLLLLLEEEEEEELLLLLLLLLHHHHHHHHHHHLLHHHHLL ESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQALSQPGTTLRVLCLGDCEVTNSGCSSLASLLLANRSLRELDL 65766771365554034675421654433056661778999988407888851138 LLLLLLLHHHHHHHLLLLLLLLHHHHHHHLLLLLLHHHHHHHHHHHLLLLLLLELL SNNCVGDPGVLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS
