Task 3: odba human Sequence-based predictions
From Bioinformatikpedia
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
Q08209 Reliability( 0-9 (most reliable) ) sec-structure AA-sequence 9888511664455661466520588761225577627887133322010123575211247777614640222244420133525663200001133420 LLLLLLLLLLLLLLLLEEEEELLLLLLLEEEEEEELLLLLLEEEEEHHHELLLLLLLEEEEEEEEELLLLEEELLLLLLLLLLLEEEEELLLLHHHHHHE MSEPKAIDPKLSTTDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESVALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMK 1331577766237775323055315633101345543037640577623532202211441221344665000134433220422233320340467624 EEEELLLLLLLEEEEEEEELLLLEEEEEEEHHHHHHHLLLLLEEEEEELLLLLLEEEEEEEEEEEEEEEEELHHHHHHHHHLLLLLHHHHHLLLEEEEEL LFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMDAFDCLPLAALMNQQFLCVHG 6474436343554310157887757611246217755467764332010220100255530521010002254110100100235413777501557763 LLLLLLLLHHHHHHHHLLLLLLLLLLLEEEEELLLLLLLLLLLLLLELLLLLELLEEEEELLLLEEEEHLLLLHHHHEHHHLLLLLLEEEEEELLLLLLL GLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFGNEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFP 2577760664021214631678750541456651137786315542201455324354045676554101135675567656767301776667777554 EEEEEEELLLEEEEELLLEEEEEELLLEEEEEEELLLLLLLLLLLLLEEEEEELLLLLHHHHHHHHHHHEELLLLLLLLLLLLLLLHHHHHHHHHHHHHH SLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLNICSDDELGSEEDGFDGATAAARKEVIRNKI 4421010235433046662477622277652464221277133333243232000332155875402001230153121135788877678876434554 HHHLHHEEEEEEEELLLLLEEEEELLLLLLLLLLLEELLLLEEEEEEEEEEELLHHHHLLLLLLLEEEEHHHHLLLLHHLLLLLLLLLLLLLLLLHHHHH RAIGKMARVFSVLREESESVLTLKGLTPTGMLPSGVLSGGKQTLQSATVEAIEADEAIKGFSPQHKITSFEEAKGLDRINERMPPRRDAMPSDANLNSIN 331156787677886677889 HHHLLLLLLLLLLLLLLLLLL KALTSETNGTDSNGSNSSNIQ
