Task 3: odba human Sequence-based predictions

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