1 <?xml version="1.0" encoding="UTF-8"?>
3 * This file is part of the Vamsas Client version 0.2.
4 * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
5 * Andrew Waterhouse and Dominik Lindner.
7 * Earlier versions have also been incorporated into Jalview version 2.4
8 * since 2008, and TOPALi version 2 since 2007.
10 * The Vamsas Client is free software: you can redistribute it and/or modify
11 * it under the terms of the GNU Lesser General Public License as published by
12 * the Free Software Foundation, either version 3 of the License, or
13 * (at your option) any later version.
15 * The Vamsas Client is distributed in the hope that it will be useful,
16 * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18 * GNU Lesser General Public License for more details.
20 * You should have received a copy of the GNU Lesser General Public License
21 * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
23 <VamsasDocument xmlns="http://www.vamsas.ac.uk/vamsasDocument"
24 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
25 xsi:schemaLocation="http://www.vamsas.ac.uk/vamsasDocument file:vamsasDocument.xsd">
26 <Version>alpha</Version>
27 <LockFile>some kind of resolvable session reference.</LockFile>
28 <Provenance xmlns="http://www.vamsas.org">
32 <Action>updated the xml schema</Action>
33 <Date>2006-01-17</Date>
36 <VAMSAS xmlns="http://www.vamsas.org"></VAMSAS>
37 <VAMSAS xmlns="http://www.vamsas.org" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vamsas.org
40 <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554296">
41 <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLNINVIAVQGDISNYKECEKIIKAALDKFNGIDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
44 <Sequence start="1" end="168" dictionary="vamsas:aa" id="a1127235554297">
45 <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDELRKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWLGNIGQANYSAAKAGVIGFTKTLAREL</sequence>
48 <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554298">
49 <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKLKALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGRIDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
52 <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554299">
53 <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALGFKFYVAEGDVSDFESCKAMVAKIEADLGPVDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
54 <name>NODG_AZOBR</name>
56 <Sequence start="1" end="166" dictionary="vamsas:aa" id="a1127235554300">
57 <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDIRETARMVEKEGRKALPVSTDIRVEEDVENMISEAVDAFGRIDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
60 <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554301">
61 <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYASNAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
64 <Sequence start="1" end="164" dictionary="vamsas:aa" id="a1127235554302">
65 <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKLAKVAAQLKGAEHLIRATDVADLTDVEALFKEVAERFGRLDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD</sequence>
68 <Sequence start="1" end="164" dictionary="vamsas:aa" id="a1127235554303">
69 <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQLAIVIEQFDSARVYAQKVDVSDPEQVQALVRKTVERFGRLDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD</sequence>
72 <Sequence start="1" end="163" dictionary="vamsas:aa" id="a1127235554304">
73 <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENGKGLALNVTDVESIEATLKAINDEFGAIDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
76 <Alignment gapChar="-">
77 <AlignmentAnnotation type="recombinationbreakpoint" graph="false">
78 <seg start="1" end="163" inclusive="false"/>
79 <annotationElement position="50" after="true">
80 <description>Topali Breakpoint</description>
81 <glyph dict="utf8">?</glyph>
87 <Action>added-by hand</Action>
88 <Date>2006-09-11</Date>
91 </AlignmentAnnotation>
92 <alignmentSequence start="1" end="167" refid="a1127235554296">
93 <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLN--INVIAVQGDISNYKECEKIIKAALDKFNG--IDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
96 <alignmentSequence start="1" end="168" refid="a1127235554297">
97 <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDEL--RKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWL-GNIGQANYSAAKAGVIGFTKTLAREL</sequence>
100 <alignmentSequence start="1" end="167" refid="a1127235554298">
101 <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKL--KALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGR--IDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
104 <alignmentSequence start="1" end="167" refid="a1127235554299">
105 <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALG--FKFYVAEGDVSDFESCKAMVAKIEADLGP--VDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
106 <name>NODG_AZOBR</name>
108 <alignmentSequence start="1" end="166" refid="a1127235554300">
109 <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDI--RETARMVEKEG-RKALPVSTDIRVEEDVENMISEAVDAFGR--IDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
112 <alignmentSequence start="1" end="167" refid="a1127235554301">
113 <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMG--VKAKGYASNAANFEDTAKVVEEIHKDFGR--IDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
116 <alignmentSequence start="1" end="164" refid="a1127235554302">
117 <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKL--AKVAAQLKG---AEHLIRATDVADLTDVEALFKEVAERFGR--LDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD-</sequence>
120 <alignmentSequence start="1" end="164" refid="a1127235554303">
121 <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQL--AIVIEQFDS---ARVYAQKVDVSDPEQVQALVRKTVERFGR--LDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD-</sequence>
124 <alignmentSequence start="1" end="163" refid="a1127235554304">
125 <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGA--AAISEYLG----ENGKGLALNVTDVESIEATLKAINDEFGA--IDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
132 <Action>edited</Action>
133 <Date>2005-12-21</Date>
141 <Action>edited</Action>
142 <Date>2005-11-21</Date>
147 <ApplicationData xmlns="http://www.vamsas.org" version="" name="">
148 <dataReference>name of accompanying jar entry containing data</dataReference> <!-- alternative is base64 encoded string in <data></data> -->
149 <User fullname="a user" organization="probably very little">
150 <dataReference>another accompanying jar entry or the data tag with embedded data.</dataReference>
152 <Common><dataReference>another bogus reference</dataReference></Common>
154 <ApplicationData xmlns="http://www.vamsas.org" version="alpha" name="hmm">
155 <data>somedata</data>
156 <Instance urn="hmm://myInstancetype"><dataReference>some reference</dataReference></Instance>
158 <Attachment xmlns="http://www.vamsas.org" type="HMMER2/HMM" objectref="a1127235554304" compressed="false">