Difference between revisions of "Task 3: odba human Sequence-based predictions"
From Bioinformatikpedia
(→psipred) |
(→reprof) |
||
| Line 99: | Line 99: | ||
L |
L |
||
L |
L |
||
| + | |||
| + | == DSSP_Server == |
||
| + | to use DSSP_Server we first had to determine which pdb-ID's are associated with the uniprot ID's P12694, P10775, Q9X0E6, Q08209 |
||
| + | <table> |
||
| + | <tr><td>uniprot ID</td><td>pdb ID's</td></tr> |
||
| + | <tr><td>P12694</td><td>1DTW, 1OLS, 1OLU, 1OLX, 1U5B, 1V11, 1V16, 1V1M, 1V1R, 1WCI, 1X7W, 1X7Y, 1X7Z, 1X80, 2BEU, 2BEV, 2BEW, 2BFB, 2BFC, 2BFD, 2BFE, 2BFF, 2J9F</td></tr> |
||
| + | <tr><td>P10775</td><td>1DFJ, 2BNH</td></tr> |
||
| + | <tr><td>Q08209</td><td>1AUI, 1M63, 1MF8, 2JOG, 2JZI, 2P6B, 2R28, 2W73, 3LL8</td></tr> |
||
| + | <tr><td>Q9X0E6</td><td>1KR4, 1O5J, 1VHF</td></tr> |
||
| + | </table> |
||
| + | |||
== psipred == |
== psipred == |
||
the version from [http://bioinf.cs.ucl.ac.uk/psipred/] was used to predict secondary structure with psipred. |
the version from [http://bioinf.cs.ucl.ac.uk/psipred/] was used to predict secondary structure with psipred. |
||
Revision as of 15:41, 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
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
Q9X0E6 Reliability( 0-9 (most reliable) ) sec-structure AA-sequence 7687613771687888888888877787530020104624520132330256774264687898899987508777820100246778889988877524 LEEEEELLLLHHHHHHHHHHHHHHHHHHHHLHLHHHLLLEEELEEELLHHHHHHHLLLHHHHHHHHHHHHHLLLLLLLHHEHHHHHHHHHHHHHHHHHHL MILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEEKEKELYEELRKLHPYETPAIFTLKVENVLTEYMNWLRESV 9 L L
DSSP_Server
to use DSSP_Server we first had to determine which pdb-ID's are associated with the uniprot ID's P12694, P10775, Q9X0E6, Q08209
| uniprot ID | pdb ID's |
| P12694 | 1DTW, 1OLS, 1OLU, 1OLX, 1U5B, 1V11, 1V16, 1V1M, 1V1R, 1WCI, 1X7W, 1X7Y, 1X7Z, 1X80, 2BEU, 2BEV, 2BEW, 2BFB, 2BFC, 2BFD, 2BFE, 2BFF, 2J9F |
| P10775 | 1DFJ, 2BNH |
| Q08209 | 1AUI, 1M63, 1MF8, 2JOG, 2JZI, 2P6B, 2R28, 2W73, 3LL8 |
| Q9X0E6 | 1KR4, 1O5J, 1VHF |
psipred
the version from [1] was used to predict secondary structure with psipred. Results:
obda_human confidence sec-structure AA-sequence 915554344652010125789986408888898888999867679889999999999943 CHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC MAVAIAAARVWRLNRGLSQAALLLLRQPGARGLARSHPPRQQQQFSSLDDKPQFPGASAE 345544347897889982787589997259999999999999999999799999999999 CCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH FIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILY 984258734444798615999998531399982418689312241328998999998626 HHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCEEECCCCCCHHHHHCCCCHHHHHHHHCC ESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYG 978889988877778888776122353334681566759888767099958999818886 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCC NISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGA 670358878577674079759999579823236884113641143204567987321028 CCHHHHHHHHHHHHHHCCCEEEEEECCCEEECCCCCCCCCCCHHHHHCCCCCCCCCEECC ASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDG 209999999999999999089974998642117999999999999997788866514995 CCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHCCCC NDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHP 799999999779999999999999999999999999992999996677866421799789 HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHH ISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQL 9999999999998299899998789 HHHHHHHHHHHHHHCCCCCCCCCCC RKQQESLARHLQTYGEHYPLDHFDK
P10775 confidence sec-structure AA-sequence 989828999999999999677137869971179999887999999643699967898647 CEEECCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCEEECCC MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRT 999958999999760499984138982169999455648999723799858897979999 CCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCEEECCCCCC NELGDAGVHLVLQGLQSPTCKIQKLSLQNCSLTEAGCGVLPSTLRSLPTLRELHLSDNPL 926999999884299986488981148899014899999871699979997869999968 CHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCEEECCCCCCCHH GDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELTVSNNDIGEA 999999750299985368971389999776999999882199979796999999918999 HHHHHHHHCCCCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHH GARVLGQGLADSACQLETLRLENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIA 998530499984148970289999665999999860499969996889999907999999 HHHHHHCCCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHH ELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLLC 980499986458961189789888999999882499749896999999925899999851 HHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCCHHHHHHHHHC ESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQAL 899961119980268899666999999984399979885999999938999999840699 CCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHHHCCC SQPGTTLRVLCLGDCEVTNSGCSSLASLLLANRSLRELDLSNNCVGDPGVLQLLGSLEQP 997678830589887899999999995599831219 CCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCEECC GCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS
Q08209 confidence sec-structure AA-sequence 999988999887776433454799998899321139899989999999996317799999 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHH MSEPKAIDPKLSTTDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESV 999999999997219880321498447446663057899999816999998630024543 HHHHHHHHHHHHHHCCCCEEECCCEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC ALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYV 689971899999999834099957772157432122131554799995408989999985 CCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHH DRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMD 429830331043915485046798999911110268999999999741002589999889 HCCCCHHHHHCCCCEEEEECCCCCCCCCHHHHCCCCCCCCCCCCCCCCHHCCCCCCCCCC AFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFG 976434567889874069747689999987549803433323114013201134467999 CCCCCCCCCCCCCCCCEEECCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCC NEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFP 469980378752345882379998376020786434899998898885444531367899 CEEEEECCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHH SLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEK 999999984067865568988888820389999999997775556788889999842100 HHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH VTEMLVNVLNICSDDELGSEEDGFDGATAAARKEVIRNKIRAIGKMARVFSVLREESESV 000137999999886667723566666677776665430699998898548887401200 HHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHH LTLKGLTPTGMLPSGVLSGGKQTLQSATVEAIEADEAIKGFSPQHKITSFEEAKGLDRIN 38999989998864522211113457789999999999999 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC ERMPPRRDAMPSDANLNSINKALTSETNGTDSNGSNSSNIQ
Q9X0E6 confidence sec-structure AA-sequence 999999079999999999998635611237776532476544610112148789766711 CEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEECCCEEECCEEEEEEECCCC MILVYSTFPNEEKALEIGRKLLEKRLIACFNAFEIRSGYWWKGEIVQDKEWAAIFKTTEE 19999999986599966418998366555778899875229 CHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHCC KEKELYEELRKLHPYETPAIFTLKVENVLTEYMNWLRESVL
