From Eric.Jain at isb-sib.ch Tue Sep 4 13:53:31 2007 From: Eric.Jain at isb-sib.ch (Eric Jain) Date: Tue Sep 4 13:53:49 2007 Subject: [Jalview-discuss] Jalview can't load files containing features with unknown begin or end positions Message-ID: <46DD554B.1090609@isb-sib.ch> Perhaps there is no good way to display such features in Jalview, but it might be preferable to skip such features, instead of aborting the parsing? -------------- next part -------------- CLUSTAL W 2.0 multiple sequence alignment P09535 ----------------------MGIPVGKSMLVLLISLAFAL--CCIAAYGPGETLCGGE 37 P01346 ----------------------MGIPVGKSMLVLLISLAFAL--CCIAAYRPSETLCGGE 37 P01344 ----------------------MGIPMGKSMLVLLTFLAFAS--CCIAAYRPSETLCGGE 37 P07456 ----------------------MGITAGKSVLVLLAFLAFAS--CCYAAYRPSETLCGGE 37 P10763 MGKISSLPTQLFKCCFCDFLKQVKMPVTSSSHLFYLALCLLA--FSSSATAGPETLCGAE 59 P07455 MGKISSLPTQLFKCCFCDFLKQVKMPITSSSHLFYLALCLLA--FTSSATAGPETLCGAE 59 P01343 MGKISSLPTQLFKCCFCDFLK-VKMHTMSSSHLFYLALCLLT--FTSSATAGPETLCGAE 58 P05017 MGKISSLPTQLFKICLCDFLK-IKIHIMSSSHLFYLALCLLT--FTSSTTAGPETLCGAE 58 P08025 MGKISSLPTQLFKICLCDFLK-IKIHIMSSSHLFYLALCLLT--FTSSATAGPETLCGAE 58 P05019 MGKISSLPTQLFKCCFCDFLK-VKMHTMSSSHLFYLALCLLT--FTSSATAGPETLCGAE 58 P16501 METNNNLSTQLFKCYFCDILK-LKMHKMSCIHLLYLVLCFLT--LTHSAAAGPETLCGAE 58 P18254 MEKINSLSTQLVKCCFCDFLK-VKMHTVSYIHFFYLGLCLLT--LTSSAAAGPETLCGAE 58 P01315 ------------------------MALWTRLLPLLALLALWA--PAPAQAFVNQHLCGSH 35 P01317 ------------------------MALWTRLRPLLALLALWP--PPPARAFVNQHLCGSH 35 P01308 ------------------------MALWMRLLPLLALLALWG--PDPAAAFVNQHLCGSH 35 P01322 ------------------------MALWMRFLPLLALLVLWE--PKPAQAFVKQHLCGPH 35 P01323 ------------------------MALWIRFLPLLALLILWE--PRPAQAFVKQHLCGSH 35 P26729 --------------------------MKILLAIALMLSTVMW--VSTQQPQAVHTYCGRH 33 P15410 ----------------------------MKLVMLLVVVSAML--VLGGAQTASQFYCGDF 31 P21808 --------------------------MNRPVFLVLLLTGFLC--IAAQEANVAHHYCGRH 33 P04808 ----------------------MPRLFLFHLLEFCLLLNQFSRAVAAKWKDDVIKLCGRE 39 P04090 ----------------------MPRLFFFHLLGVCLLLNQFSRAVADSWMEEVIKLCGRE 39 P01348 ----------------------MPRLFSY-LLGVWLLLSQLPREIPGQSTNDFIKACGRE 38 Q14641 ----------------------MASLFRSYLPAIWLLLSQLLR----ESLAAELRGCGPR 35 P51460 -----------------------MDPRLPAWALVLLGPALVFALGPAPTPEMREKLCGHH 38 ** P09535 LVDTLQFVCSDRGFYFSRPS--SRANRRS--RGIVEECCFRSCDLALLETYCAT-PAKSE 92 P01346 LVDTLQFVCSDRGFYFSRPS--SRANRRS--RGIVEECCFRSCDLALLETYCAT-PAKSE 92 P01344 LVDTLQFVCGDRGFYFSRPA--SRVSRRS--RGIVEECCFRSCDLALLETYCAT-PAKSE 92 P07456 LVDTLQFVCGDRGFYFSRPS--SRINRRS--RGIVEECCFRSCDLALLETYCAT-PAKSE 92 P10763 LVDALQFVCGDRGFYFNKPTGYGSSSRRAPQTGIVDECCFRSCDLRRLEMYCA--PLKAA 117 P07455 LVDALQFVCGDRGFYFNKPTGYGSSSRRAPQTGIVDECCFRSCDLRRLEMYCA--PLKPA 117 P01343 LVDALQFVCGDRGFYFNKPTGYGSSSRRAPQTGIVDECCFRSCDLRRLEMYCA--PLKPA 116 P05017 LVDALQFVCGPRGFYFNKPTGYGSSIRRAPQTGIVDECCFRSCDLRRLEMYCA--PLKPT 116 P08025 LVDALQFVCGPRGFYFNKPTGYGSSIRRAPQTGIVDECCFRSCDLRRLEMYCA--PLKPT 116 P05019 LVDALQFVCGDRGFYFNKPTGYGSSSRRAPQTGIVDECCFRSCDLRRLEMYCA--PLKPA 116 P16501 LVDTLQFVCGDRGFYFSKPTGYGSNNRRSHHRGIVDECCFQSCDFRRLEMYCA--PAKQA 116 P18254 LVDALQFVCGDRGFYFSKPTGYGSSSRRLHHKGIVDECCFQSCDLRRLEMYCA--PIKPP 116 P01315 LVEALYLVCGERGFFYTPKA--RREAENPQAGAVELGGGLGG--LQALALEGPP-QKRGI 90 P01317 LVEALYLVCGERGFFYTPKA--RREVEGPQVGALELAGGPG-----AGGLEGPP-QKRGI 87 P01308 LVEALYLVCGERGFFYTPKT--RREAEDLQVGQVELGGGPGAGSLQPLALEGSL-QKRGI 92 P01322 LVEALYLVCGERGFFYTPKS--RREVEDPQVPQLELGGGPEAGDLQTLALEVAR-QKRGI 92 P01323 LVEALYLVCGERGFFYTPMS--RREVEDPQVAQLELGGGPGAGDLQTLALEVAR-QKRGI 92 P26729 LARTLADLCWEAGVDKRSGA--QFASY---GSAWLMP--YSE----------GR-GKRGI 75 P15410 LARTMSSLCWSD-MQKRSGS--QYAGY---GWPWLPP--FSS----------SR-GKRGI 72 P21808 LANTLADLCWDTSVEKRSES--SLASYSSRGWPWLPTPNFNKR---------AI-KKRGV 81 P04808 LVRAQIAICGMSTWSKRSLSQEDAPQTPRPVAEIVPSFINKDTETIIIMLEFIANLPPEL 99 P04090 LVRAQIAICGMSTWSKRSLSQEDAPQTPRPVAEIVPSFINKDTETINMMSEFVANLPQEL 99 P01348 LVRLWVEICGSVSWGRTALSLEEPQLETGPPAETMPSSITKDAEILKMMLEFVPNLPQEL 98 Q14641 FGKHLLSYCPMPEKTFTTTPG-GWLLESGRPKEMVSTSNNKDGQALGTTSEFIPNLSPEL 94 P51460 FVRALVRVCGGPRWSTEARRPAAGGDRELLQWLERRHLLHGLVADSNLTLGPGLQPLPQT 98 : * P09535 RDVSTSQAVLPDDFPRYPVG-----------------KFFQYDTWRQSAGRLRRGLPALL 135 P01346 RDVSTSQAVLPDDFPRYPVG-----------------KFFKFDTWRQSAGRLRRGLPALL 135 P01344 RDVSTPPTVLPDNFPRYPVG-----------------KFFQYDTWKQSTQRLRRGLPALL 135 P07456 RDVSASTTVLPDDVTAYPVG-----------------KFFQYDIWKQSTQRLRRGLPAFL 135 P10763 KSARSVRAQRHTDMPKAQK-------------------EVH-----------------LK 141 P07455 KSARSVRAQRHTDMPKAQK-------------------EVH-----------------LK 141 P01343 KSARSVRAQRHTDMPKTQK-------------------EVH-----------------LK 140 P05017 KAARSIRAQRHTDMPKTQK-------------------EVH-----------------LK 140 P08025 KSARSIRAQRHTDMPKTQK-------------------EVH-----------------LK 140 P05019 KSARSVRAQRHTDMPKTQKYQPPSTNKNTKSQRRKGWPKTHPGGEQKEGTEASLQIRGKK 176 P16501 KSARSVRTQRHTDMPKAQK-------------------EVH-----------------PK 140 P18254 KSARSVRAQRHTDMPKAQK-------------------EVH-----------------LK 140 P01315 VEQCCTSICSLYQLENYCN----------------------------------------- 109 P01317 VEQCCASVCSLYQLENYCN----------------------------------------- 106 P01308 VEQCCTSICSLYQLENYCN----------------------------------------- 111 P01322 VDQCCTSICSLYQLENYCN----------------------------------------- 111 P01323 VDQCCTSICSLYQLENYCN----------------------------------------- 111 P26729 VDECCLRPCSVDVLLSYC------------------------------------------ 93 P15410 VDECCYRPCTIDVLMSYCDN---------------------------------------- 92 P21808 VDECCIQPCTLDVLATYC------------------------------------------ 99 P04808 KAALSERQPSLPELQQYVPA-------------------LKDSNLSFEEFKKLIRNRQSE 140 P04090 KLTLSEMQPALPQLQQHVPV-------------------LKDSSLLFEEFKKLIRNRQSE 140 P01348 KATLSERQPSLRELQQSAS---------------------KDSNLNFEEFKKIILNRQNE 137 Q14641 KKPLSEGQPSLKKIILSRK----------------------------------------K 114 P51460 SHHHRHHRAAATNPARYCCLS--------------------------------------G 120 P09535 RARRGRMLAKELKEFREAKRHRPLIVLPPKDPA-HGGASSEMSSNHQ 181 P01346 RARRGRMLAKELEAFREAKRHRPLIVLPPKDPA-HGGASSEMSSNHQ 181 P01344 RARRGHVLAKELEAFREAKRHRPLIALPTQDPA-HGGAPPEMASNRK 181 P07456 RARRGRTLAKELEALREAKSHRPLIALPTQDPATHGGASSKASSD-- 180 P10763 NTSRGSAGNKNYRM--------------------------------- 155 P07455 NTSRGSAGNKNYRM--------------------------------- 155 P01343 NASRGSAGNKNYRM--------------------------------- 154 P05017 NTSRGSAGNKTYRM--------------------------------- 154 P08025 NTSRGSAGNKTYRM--------------------------------- 154 P05019 KEQRREIGSRNAECRGKKGK--------------------------- 196 P16501 NTSRGNTGSRGFRM--------------------------------- 154 P18254 NTSRGNTGNRNYRM--------------------------------- 154 P01315 ----------------------------------------------- P01317 ----------------------------------------------- P01308 ----------------------------------------------- P01322 ----------------------------------------------- P01323 ----------------------------------------------- P26729 ----------------------------------------------- P15410 ----------------------------------------------- P21808 ----------------------------------------------- P04808 AADSNPSELKYLGLDTHSQKKRRPYVALFEKCCLIGCTKRSLAKYC- 186 P04090 AADSSPSELKYLGLDTHSRKKRQLYSALANKCCHVGCTKRSLARFC- 186 P01348 AEDKSLLELKNLGLDKHSRKKRLFRMTLSEKCCQVGCIRKDIARLC- 183 Q14641 RSGRHRFDPFCCEVICDDGTSVKLCT--------------------- 140 P51460 CTQQDLLTLCPY----------------------------------- 132 -------------- next part -------------- ##gff-version 3 ##sequence-region P26729 1 92 P26729 UniProtKB Signal peptide 1 19 . . . . P26729 UniProtKB Peptide 20 47 . . . ID=PRO_0000015977;Note=Bombyxin A-6 B chain P26729 UniProtKB Propeptide 50 70 . . . ID=PRO_0000015978;Note=C peptide like P26729 UniProtKB Peptide 73 92 . . . ID=PRO_0000015979;Note=Bombyxin A-6 A chain P26729 UniProtKB Modified residue 20 20 . . . Note=Pyrrolidone carboxylic acid P26729 UniProtKB Disulfide bond 29 79 . . . Note=Interchain (between B and A chains) P26729 UniProtKB Disulfide bond 41 92 . . . Note=Interchain (between B and A chains) P26729 UniProtKB Disulfide bond 78 83 . . . . P26729 UniProtKB Turn 32 35 . . . . P26729 UniProtKB Helix 36 38 . . . . P26729 UniProtKB Helix 40 43 . . . . ##sequence-region P15410 1 91 P15410 UniProtKB Signal peptide 1 19 . . . Status=Potential P15410 UniProtKB Peptide 20 44 . . . ID=PRO_0000016025;Note=Bombyxin C-1 B chain P15410 UniProtKB Propeptide 47 67 . . . ID=PRO_0000016026;Note=C peptide like P15410 UniProtKB Peptide 70 91 . . . ID=PRO_0000016027;Note=Bombyxin C-1 A chain P15410 UniProtKB Modified residue 20 20 . . . Note=Pyrrolidone carboxylic acid;Status=Potential P15410 UniProtKB Disulfide bond 27 76 . . . Note=Interchain (between B and A chains);Status=By similarity P15410 UniProtKB Disulfide bond 39 89 . . . Note=Interchain (between B and A chains);Status=By similarity P15410 UniProtKB Disulfide bond 75 80 . . . Status=By similarity ##sequence-region P21808 1 98 P21808 UniProtKB Signal peptide 1 19 . . . . P21808 UniProtKB Peptide 20 47 . . . ID=PRO_0000016034;Note=Bombyxin E-1 B chain P21808 UniProtKB Propeptide 50 75 . . . ID=PRO_0000016035;Note=C peptide like P21808 UniProtKB Peptide 79 98 . . . ID=PRO_0000016036;Note=Bombyxin E-1 A chain P21808 UniProtKB Modified residue 20 20 . . . Note=Pyrrolidone carboxylic acid P21808 UniProtKB Disulfide bond 29 85 . . . Note=Interchain (between B and A chains) P21808 UniProtKB Disulfide bond 41 98 . . . Note=Interchain (between B and A chains) P21808 UniProtKB Disulfide bond 84 89 . . . . ##sequence-region P07455 1 154 P07455 UniProtKB Signal peptide 1 . . . . Status=Potential P07455 UniProtKB Propeptide . 49 . . . ID=PRO_0000015647 P07455 UniProtKB Chain 50 119 . . . ID=PRO_0000015648;Note=Insulin-like growth factor I P07455 UniProtKB Propeptide 120 154 . . . ID=PRO_0000015649;Note=E peptide P07455 UniProtKB Region 50 78 . . . Note=B P07455 UniProtKB Region 79 90 . . . Note=C P07455 UniProtKB Region 91 111 . . . Note=A P07455 UniProtKB Region 112 119 . . . Note=D P07455 UniProtKB Disulfide bond 55 97 . . . Status=By similarity P07455 UniProtKB Disulfide bond 67 110 . . . Status=By similarity P07455 UniProtKB Disulfide bond 96 101 . . . Status=By similarity ##sequence-region P18254 1 153 P18254 UniProtKB Signal peptide 1 . . . . . P18254 UniProtKB Propeptide . 48 . . . ID=PRO_0000015690 P18254 UniProtKB Chain 49 118 . . . ID=PRO_0000015691;Note=Insulin-like growth factor I P18254 UniProtKB Propeptide 119 153 . . . ID=PRO_0000015692;Note=E peptide P18254 UniProtKB Region 49 77 . . . Note=B P18254 UniProtKB Region 78 89 . . . Note=C P18254 UniProtKB Region 90 110 . . . Note=A P18254 UniProtKB Region 111 118 . . . Note=D P18254 UniProtKB Disulfide bond 54 96 . . . Status=By similarity P18254 UniProtKB Disulfide bond 66 109 . . . Status=By similarity P18254 UniProtKB Disulfide bond 95 100 . . . Status=By similarity ##sequence-region P05017 1 153 P05017 UniProtKB Signal peptide 1 . . . . Status=Potential P05017 UniProtKB Propeptide . 48 . . . ID=PRO_0000015666;Status=By similarity P05017 UniProtKB Chain 49 118 . . . ID=PRO_0000015667;Note=Insulin-like growth factor I P05017 UniProtKB Propeptide 119 153 . . . ID=PRO_0000015668;Note=E peptide P05017 UniProtKB Region 49 77 . . . Note=B P05017 UniProtKB Region 78 89 . . . Note=C P05017 UniProtKB Region 90 110 . . . Note=A P05017 UniProtKB Region 111 118 . . . Note=D P05017 UniProtKB Disulfide bond 54 96 . . . Status=By similarity P05017 UniProtKB Disulfide bond 66 109 . . . Status=By similarity P05017 UniProtKB Disulfide bond 95 100 . . . Status=By similarity ##sequence-region P08025 1 153 P08025 UniProtKB Signal peptide 1 . . . . Status=Potential P08025 UniProtKB Propeptide . 48 . . . ID=PRO_0000015681 P08025 UniProtKB Chain 49 118 . . . ID=PRO_0000015682;Note=Insulin-like growth factor I P08025 UniProtKB Propeptide 119 153 . . . ID=PRO_0000015683;Note=E peptide P08025 UniProtKB Region 49 77 . . . Note=B P08025 UniProtKB Region 78 89 . . . Note=C P08025 UniProtKB Region 90 110 . . . Note=A P08025 UniProtKB Region 111 118 . . . Note=D P08025 UniProtKB Disulfide bond 54 96 . . . Status=By similarity P08025 UniProtKB Disulfide bond 66 109 . . . Status=By similarity P08025 UniProtKB Disulfide bond 95 100 . . . Status=By similarity ##sequence-region P10763 1 154 P10763 UniProtKB Signal peptide 1 . . . . . P10763 UniProtKB Propeptide . 49 . . . ID=PRO_0000015684 P10763 UniProtKB Chain 50 119 . . . ID=PRO_0000015685;Note=Insulin-like growth factor I P10763 UniProtKB Propeptide 120 154 . . . ID=PRO_0000015686;Note=E peptide P10763 UniProtKB Region 50 78 . . . Note=B P10763 UniProtKB Region 79 90 . . . Note=C P10763 UniProtKB Region 91 111 . . . Note=A P10763 UniProtKB Region 112 119 . . . Note=D P10763 UniProtKB Disulfide bond 55 97 . . . Status=By similarity P10763 UniProtKB Disulfide bond 67 110 . . . Status=By similarity P10763 UniProtKB Disulfide bond 96 101 . . . Status=By similarity ##sequence-region P01343 1 153 P01343 UniProtKB Signal peptide 1 21 . . . Status=Potential P01343 UniProtKB Propeptide 22 48 . . . ID=PRO_0000015660 P01343 UniProtKB Chain 49 118 . . . ID=PRO_0000015661;Note=Insulin-like growth factor IA P01343 UniProtKB Propeptide 119 153 . . . ID=PRO_0000015662;Note=E peptide P01343 UniProtKB Region 49 77 . . . Note=B P01343 UniProtKB Region 78 89 . . . Note=C P01343 UniProtKB Region 90 110 . . . Note=A P01343 UniProtKB Region 111 118 . . . Note=D P01343 UniProtKB Disulfide bond 54 96 . . . . P01343 UniProtKB Disulfide bond 66 109 . . . . P01343 UniProtKB Disulfide bond 95 100 . . . . P01343 UniProtKB Helix 52 66 . . . . P01343 UniProtKB Helix 67 69 . . . . P01343 UniProtKB Helix 75 95 . . . . P01343 UniProtKB Beta strand 96 98 . . . . P01343 UniProtKB Helix 102 108 . . . . ##sequence-region P16501 1 153 P16501 UniProtKB Signal peptide 1 . . . . . P16501 UniProtKB Propeptide . 48 . . . ID=PRO_0000015708 P16501 UniProtKB Chain 49 118 . . . ID=PRO_0000015709;Note=Insulin-like growth factor I-A P16501 UniProtKB Propeptide 119 153 . . . ID=PRO_0000015710;Note=E peptide P16501 UniProtKB Region 49 77 . . . Note=B P16501 UniProtKB Region 78 89 . . . Note=C P16501 UniProtKB Region 90 110 . . . Note=A P16501 UniProtKB Region 111 118 . . . Note=D P16501 UniProtKB Disulfide bond 54 96 . . . Status=By similarity P16501 UniProtKB Disulfide bond 66 109 . . . Status=By similarity P16501 UniProtKB Disulfide bond 95 100 . . . Status=By similarity ##sequence-region P05019 1 195 P05019 UniProtKB Signal peptide 1 21 . . . Status=Potential P05019 UniProtKB Propeptide 22 48 . . . ID=PRO_0000015663 P05019 UniProtKB Chain 49 118 . . . ID=PRO_0000015664;Note=Insulin-like growth factor IB P05019 UniProtKB Propeptide 119 195 . . . ID=PRO_0000015665;Note=E peptide P05019 UniProtKB Region 49 77 . . . Note=B P05019 UniProtKB Region 78 89 . . . Note=C P05019 UniProtKB Region 90 110 . . . Note=A P05019 UniProtKB Region 111 118 . . . Note=D P05019 UniProtKB Disulfide bond 54 96 . . . . P05019 UniProtKB Disulfide bond 66 109 . . . . P05019 UniProtKB Disulfide bond 95 100 . . . . P05019 UniProtKB Helix 55 66 . . . . P05019 UniProtKB Helix 67 69 . . . . P05019 UniProtKB Beta strand 73 76 . . . . P05019 UniProtKB Beta strand 87 90 . . . . P05019 UniProtKB Helix 91 95 . . . . P05019 UniProtKB Turn 96 98 . . . . P05019 UniProtKB Helix 102 106 . . . . ##sequence-region P07456 1 179 P07456 UniProtKB Signal peptide 1 24 . . . . P07456 UniProtKB Chain 25 91 . . . ID=PRO_0000015711;Note=Insulin-like growth factor II P07456 UniProtKB Propeptide 92 179 . . . ID=PRO_0000015712;Note=E peptide P07456 UniProtKB Region 25 52 . . . Note=B P07456 UniProtKB Region 53 64 . . . Note=C P07456 UniProtKB Region 65 85 . . . Note=A P07456 UniProtKB Region 86 91 . . . Note=D P07456 UniProtKB Disulfide bond 33 71 . . . Status=By similarity P07456 UniProtKB Disulfide bond 45 84 . . . Status=By similarity P07456 UniProtKB Disulfide bond 70 75 . . . Status=By similarity ##sequence-region P01344 1 180 P01344 UniProtKB Signal peptide 1 24 . . . . P01344 UniProtKB Chain 25 91 . . . ID=PRO_0000015717;Note=Insulin-like growth factor II P01344 UniProtKB Chain 26 91 . . . ID=PRO_0000015718;Note=Insulin-like growth factor II Ala-25 Del P01344 UniProtKB Propeptide 92 180 . . . ID=PRO_0000015719;Note=E peptide P01344 UniProtKB Region 25 52 . . . Note=B P01344 UniProtKB Region 53 64 . . . Note=C P01344 UniProtKB Region 65 85 . . . Note=A P01344 UniProtKB Region 86 91 . . . Note=D P01344 UniProtKB Glycosylation 99 99 . . . Note=O-linked (GalNAc...) P01344 UniProtKB Disulfide bond 33 71 . . . . P01344 UniProtKB Disulfide bond 45 84 . . . . P01344 UniProtKB Disulfide bond 70 75 . . . . P01344 UniProtKB Helix 35 45 . . . . P01344 UniProtKB Helix 46 48 . . . . P01344 UniProtKB Beta strand 57 59 . . . . P01344 UniProtKB Helix 66 70 . . . . P01344 UniProtKB Helix 77 80 . . . . P01344 UniProtKB Helix 81 83 . . . . ##sequence-region P09535 1 180 P09535 UniProtKB Signal peptide 1 24 . . . . P09535 UniProtKB Chain 25 91 . . . ID=PRO_0000015720;Note=Insulin-like growth factor II P09535 UniProtKB Propeptide 92 180 . . . ID=PRO_0000015721;Note=E peptide P09535 UniProtKB Region 25 52 . . . Note=B P09535 UniProtKB Region 53 64 . . . Note=C P09535 UniProtKB Region 65 85 . . . Note=A P09535 UniProtKB Region 86 91 . . . Note=D P09535 UniProtKB Disulfide bond 33 71 . . . Status=By similarity P09535 UniProtKB Disulfide bond 45 84 . . . Status=By similarity P09535 UniProtKB Disulfide bond 70 75 . . . Status=By similarity ##sequence-region P01346 1 180 P01346 UniProtKB Signal peptide 1 24 . . . . P01346 UniProtKB Chain 25 91 . . . ID=PRO_0000015729;Note=Insulin-like growth factor II P01346 UniProtKB Propeptide 92 180 . . . ID=PRO_0000015730;Note=E peptide P01346 UniProtKB Region 25 52 . . . Note=B P01346 UniProtKB Region 53 64 . . . Note=C P01346 UniProtKB Region 65 85 . . . Note=A P01346 UniProtKB Region 86 91 . . . Note=D P01346 UniProtKB Disulfide bond 33 71 . . . Status=By similarity P01346 UniProtKB Disulfide bond 45 84 . . . Status=By similarity P01346 UniProtKB Disulfide bond 70 75 . . . Status=By similarity ##sequence-region P01322 1 110 P01322 UniProtKB Signal peptide 1 24 . . . . P01322 UniProtKB Peptide 25 54 . . . ID=PRO_0000015895;Note=Insulin-1 B chain P01322 UniProtKB Propeptide 57 87 . . . ID=PRO_0000015896;Note=C peptide P01322 UniProtKB Peptide 90 110 . . . ID=PRO_0000015897;Note=Insulin-1 A chain P01322 UniProtKB Disulfide bond 31 96 . . . Note=Interchain (between B and A chains) P01322 UniProtKB Disulfide bond 43 109 . . . Note=Interchain (between B and A chains) P01322 UniProtKB Disulfide bond 95 100 . . . . ##sequence-region P01323 1 110 P01323 UniProtKB Signal peptide 1 24 . . . . P01323 UniProtKB Peptide 25 54 . . . ID=PRO_0000015898;Note=Insulin-2 B chain P01323 UniProtKB Propeptide 57 87 . . . ID=PRO_0000015899;Note=C peptide P01323 UniProtKB Peptide 90 110 . . . ID=PRO_0000015900;Note=Insulin-2 A chain P01323 UniProtKB Disulfide bond 31 96 . . . Note=Interchain (between B and A chains) P01323 UniProtKB Disulfide bond 43 109 . . . Note=Interchain (between B and A chains) P01323 UniProtKB Disulfide bond 95 100 . . . . ##sequence-region P01317 1 105 P01317 UniProtKB Signal peptide 1 24 . . . . P01317 UniProtKB Peptide 25 54 . . . ID=PRO_0000015764;Note=Insulin B chain P01317 UniProtKB Propeptide 57 82 . . . ID=PRO_0000015765;Note=C peptide P01317 UniProtKB Peptide 85 105 . . . ID=PRO_0000015766;Note=Insulin A chain P01317 UniProtKB Disulfide bond 31 91 . . . Note=Interchain (between B and A chains) P01317 UniProtKB Disulfide bond 43 104 . . . Note=Interchain (between B and A chains) P01317 UniProtKB Disulfide bond 90 95 . . . . P01317 UniProtKB Helix 32 43 . . . . P01317 UniProtKB Helix 44 46 . . . . P01317 UniProtKB Helix 86 90 . . . . P01317 UniProtKB Helix 97 101 . . . . ##sequence-region P01308 1 110 P01308 UniProtKB Signal peptide 1 24 . . . . P01308 UniProtKB Peptide 25 54 . . . ID=PRO_0000015819;Note=Insulin B chain P01308 UniProtKB Propeptide 57 87 . . . ID=PRO_0000015820;Note=C peptide P01308 UniProtKB Peptide 90 110 . . . ID=PRO_0000015821;Note=Insulin A chain P01308 UniProtKB Disulfide bond 31 96 . . . Note=Interchain (between B and A chains) P01308 UniProtKB Disulfide bond 43 109 . . . Note=Interchain (between B and A chains) P01308 UniProtKB Disulfide bond 95 100 . . . . P01308 UniProtKB Helix 35 43 . . . . P01308 UniProtKB Helix 44 46 . . . . P01308 UniProtKB Beta strand 48 50 . . . . P01308 UniProtKB Beta strand 56 58 . . . . P01308 UniProtKB Beta strand 74 76 . . . . P01308 UniProtKB Helix 79 81 . . . . P01308 UniProtKB Turn 84 86 . . . . P01308 UniProtKB Helix 91 95 . . . . P01308 UniProtKB Helix 105 108 . . . . ##sequence-region P01315 1 108 P01315 UniProtKB Signal peptide 1 24 . . . . P01315 UniProtKB Peptide 25 54 . . . ID=PRO_0000015879;Note=Insulin B chain P01315 UniProtKB Propeptide 57 85 . . . ID=PRO_0000015880;Note=C peptide P01315 UniProtKB Peptide 88 108 . . . ID=PRO_0000015881;Note=Insulin A chain P01315 UniProtKB Disulfide bond 31 94 . . . Note=Interchain (between B and A chains) P01315 UniProtKB Disulfide bond 43 107 . . . Note=Interchain (between B and A chains) P01315 UniProtKB Disulfide bond 93 98 . . . . P01315 UniProtKB Helix 33 43 . . . . P01315 UniProtKB Helix 44 46 . . . . P01315 UniProtKB Beta strand 48 50 . . . . P01315 UniProtKB Helix 89 95 . . . . P01315 UniProtKB Helix 100 103 . . . . P01315 UniProtKB Helix 104 106 . . . . ##sequence-region P51460 1 131 P51460 UniProtKB Signal peptide 1 20 . . . . P51460 UniProtKB Peptide 21 55 . . . ID=PRO_0000016140;Note=Insulin-like 3 B chain P51460 UniProtKB Propeptide 58 104 . . . ID=PRO_0000016141;Note=C peptide like;Status=Potential P51460 UniProtKB Peptide 106 131 . . . ID=PRO_0000016142;Note=Insulin-like 3 A chain P51460 UniProtKB Disulfide bond 34 116 . . . Note=Interchain (between B and A chains);Status=By similarity P51460 UniProtKB Disulfide bond 46 129 . . . Note=Interchain (between B and A chains);Status=By similarity P51460 UniProtKB Disulfide bond 115 120 . . . Status=By similarity ##sequence-region Q14641 1 139 Q14641 UniProtKB Signal peptide 1 25 . . . . Q14641 UniProtKB Chain 26 139 . . . ID=PRO_0000016155;Note=Early placenta insulin-like peptide Q14641 UniProtKB Peptide 26 58 . . . ID=PRO_0000016156;Note=Early placenta insulin-like peptide B chain Q14641 UniProtKB Propeptide 59 114 . . . ID=PRO_0000016157;Note=C peptide Q14641 UniProtKB Peptide 115 139 . . . ID=PRO_0000016158;Note=Early placenta insulin-like peptide A chain Q14641 UniProtKB Disulfide bond 31 125 . . . Note=Interchain (between B and A chains);Status=By similarity Q14641 UniProtKB Disulfide bond 43 138 . . . Note=Interchain (between B and A chains);Status=By similarity Q14641 UniProtKB Disulfide bond 124 129 . . . Status=By similarity ##sequence-region P04808 1 185 P04808 UniProtKB Signal peptide 1 22 . . . Status=By similarity P04808 UniProtKB Peptide 23 53 . . . ID=PRO_0000016076;Note=Relaxin B chain;Status=By similarity P04808 UniProtKB Propeptide 56 158 . . . ID=PRO_0000016077;Note=Connecting peptide;Status=By similarity P04808 UniProtKB Peptide 163 185 . . . ID=PRO_0000016078;Note=Relaxin A chain;Status=By similarity P04808 UniProtKB Disulfide bond 35 172 . . . Note=Interchain (between B and A chains);Status=By similarity P04808 UniProtKB Disulfide bond 47 185 . . . Note=Interchain (between B and A chains);Status=By similarity P04808 UniProtKB Disulfide bond 171 176 . . . Status=By similarity ##sequence-region P04090 1 185 P04090 UniProtKB Signal peptide 1 24 . . . . P04090 UniProtKB Peptide 25 53 . . . ID=PRO_0000016079;Note=Relaxin B chain P04090 UniProtKB Propeptide 56 157 . . . ID=PRO_0000016080;Note=Connecting peptide P04090 UniProtKB Peptide 162 185 . . . ID=PRO_0000016081;Note=Relaxin A chain P04090 UniProtKB Modified residue 162 162 . . . Note=Pyrrolidone carboxylic acid P04090 UniProtKB Disulfide bond 35 172 . . . Note=Interchain (between B and A chains) P04090 UniProtKB Disulfide bond 47 185 . . . Note=Interchain (between B and A chains) P04090 UniProtKB Disulfide bond 171 176 . . . . P04090 UniProtKB Helix 27 29 . . . . P04090 UniProtKB Helix 36 49 . . . . P04090 UniProtKB Helix 163 173 . . . . P04090 UniProtKB Helix 178 182 . . . . ##sequence-region P01348 1 182 P01348 UniProtKB Signal peptide 1 24 . . . . P01348 UniProtKB Peptide 25 56 . . . ID=PRO_0000016112;Note=Relaxin B chain P01348 UniProtKB Propeptide 57 154 . . . ID=PRO_0000016113;Note=Connecting peptide P01348 UniProtKB Propeptide 159 160 . . . ID=PRO_0000016114 P01348 UniProtKB Peptide 161 182 . . . ID=PRO_0000016115;Note=Relaxin A chain P01348 UniProtKB Modified residue 25 25 . . . Note=Pyrrolidone carboxylic acid P01348 UniProtKB Disulfide bond 34 169 . . . Note=Interchain (between B and A chains) P01348 UniProtKB Disulfide bond 46 182 . . . Note=Interchain (between B and A chains) P01348 UniProtKB Disulfide bond 168 173 . . . . P01348 UniProtKB Helix 36 46 . . . . P01348 UniProtKB Helix 47 49 . . . . P01348 UniProtKB Helix 164 168 . . . . P01348 UniProtKB Helix 175 178 . . . . P01348 UniProtKB Helix 179 181 . . . . From jimp at compbio.dundee.ac.uk Tue Sep 4 14:30:49 2007 From: jimp at compbio.dundee.ac.uk (Jim Procter) Date: Tue Sep 4 14:30:50 2007 Subject: [Jalview-discuss] Jalview can't load files containing features with unknown begin or end positions In-Reply-To: <46DD554B.1090609@isb-sib.ch> References: <46DD554B.1090609@isb-sib.ch> Message-ID: <46DD5E09.9050207@compbio.dundee.ac.uk> Hi Eric. Eric Jain wrote: > Perhaps there is no good way to display such features in Jalview, but > it might be preferable to skip such features, instead of aborting the > parsing? Actually, features with no start and end position are coped with from other formats - in particular its part of the DAS standard. The gff file contains periods in the blank positions (Is that actually part of the standard or would they normally be left blank?). Jalview is trying to parse the field as a number and bailing out when that fails. A couple of additional try/catch blocks fixed the problem - and this will be in the next release. Jim From Eric.Jain at isb-sib.ch Tue Sep 4 14:36:13 2007 From: Eric.Jain at isb-sib.ch (Eric Jain) Date: Tue Sep 4 14:36:36 2007 Subject: [Jalview-discuss] Jalview can't load files containing features with unknown begin or end positions In-Reply-To: <46DD5E09.9050207@compbio.dundee.ac.uk> References: <46DD554B.1090609@isb-sib.ch> <46DD5E09.9050207@compbio.dundee.ac.uk> Message-ID: <46DD5F4D.4020406@isb-sib.ch> Jim Procter wrote: > Actually, features with no start and end position are coped with from > other formats - in particular its part of the DAS standard. > > The gff file contains periods in the blank positions (Is that actually > part of the standard or would they normally be left blank?). The gff spec doesn't seem to have any examples with unknown positions, but in general they do put dots in empty fields... > Jalview is > trying to parse the field as a number and bailing out when that fails. > > A couple of additional try/catch blocks fixed the problem - and this > will be in the next release. Great, thanks!