Contents
Contents
New File/Dataset Structure
Version 1.3 of the GRAIL server is a re-engineered, highly modular server with a consistent client interface. Input to and output from the server is in the form of structured, tagged files. An example request is shown below (only a portion of the DNA sequence is shown):
[Request_grail1exons_human_1.3] [Start DNASequence] GGATCCGCTT GGAGCCCGAG GGGAAAGATT GCAAGGGACG TCCCAGGGAG CAAAGCCCCG CAGCGTGGCC GGGGACTCGG GGACCCACCC CAGCTCCGGC ... [End DNASequence] [End_Request]A complete guide to the features, organisms, and processing options and parameters is given at the end of this document. Anyone can build a client which makes a socket connection to the server host and port (currently
galahad.lsd.ornl.gov:2050) and sends a proper structured
request.
Output from the server, which we'll refer to as a GRAIL dataset,
has a similar appearance. For example, the results for the above
request are:
[Start grail1exons_human_1.3] [Seqlen= 3583] [Start exons] [Num=8] f 0 911 1001 853 1116 6.866 excellent f 2 1091 1361 954 1445 22.834 excellent f 0 1651 2071 1594 2148 39.331 excellent f 1 2181 2351 2135 2419 16.099 excellent f 1 2441 2581 2420 2587 13.010 excellent r 2 3051 3101 2913 3356 2.692 good r 0 2791 2831 2638 3138 1.672 marginal r 0 821 871 802 918 4.588 good [End exons] [End grail1_revprob_human_1.3] [End grail1exons_human_1.3]All GRAIL server clients, including the XView and Motif applications and the Web interface process these GRAIL datasets. The
xgr files stored by the XView and Motif applications
contain GRAIL datasets. The structure allows for addition of blocks
for features at will.
Downloading Grail Datasets
Clicking the DOWNLOAD button on the Result Form
will cause the Web server to download the GRAIL dataset to your machine
with a MIME type/subtype of application/x-grail-dataset.
Unless you have mapped in your Web browser a viewer for
application/x-grail-dataset (which you shouldn't!!), you
will get a file save dialog with which you can identify or name a file
for saving the GRAIL dataset.
Saved datasets may be uploaded to the Result Form or used with
the XView or Motif client applications.
The old download facility has been abandoned in favor of the new
Near the top of the Result Form is a section labeled Analysis
Results, under which is a scrollable text area with the title
Feature List. In this text area a formatted view of the feature
and options selected in the Grail Form is displayed. Example results
for feature
This information is intended for the client application developer wanting
to know how to build valid requests for the GRAIL server. There are
8 features and 5 modeled organisms. Associated with each feature are
one or more options and possibly parameters. The table below attempts
to describe supported combinations.
Options and parameters for the various features are described in the
following table.
GRAIL service requests are shown below. Italics indicate places where
substitutions are made. For example, FtrLabel and
OrgLabel correspond to the feature and organism labels,
respectively. The current version for all services is 1.3.
Blank lines are optional.
Note that OrgLabel is not supplied in the request tag for
features
Also note that for
Uploading Sequence Files and Grail Datasets
multipart/form-data encoding and the file
form input type supported by Netscape Navigator and other
browsers. The file input includes a Browse..
button which brings up a file open dialog. You may select a file from
the dialog or enter a valid name in the text box. Pressing the
Upload File button on the form causes the sequence or dataset
file to be uploaded to the Web server, which then generates a new form
using the contents of the uploaded file.
Analysis Results Display and Feature Selection
grail2exons with organism droso
and options Shadow Exons, Clusters, and
Protein Translation follows:
[Exons]
St Fr Start End ORFstart ORFend Score Quality
1- r 2 2136 2708 2136 2708 74.000 excellent
2- r 1 1499 2023 1481 2023 35.000 marginal
3- r 1 1019 1462 1001 1462 74.000 excellent
[Shadow Exons]
St Fr Start End ORFstart ORFend Score Quality
4- f 2 1053 1445 954 1445 50.000 good
5- f 0 1651 2148 1594 2148 44.000 good
6- f 1 2171 2350 2135 2419 89.000 excellent
7- f 1 2444 2587 2420 2587 75.000 excellent
[Exon Translations]
8- MSEIKPGEKMTGERTGGARASAEPHLSHLLSVGLGVQGGLGQQHWVLLRG
HAQLVVEGVVPDLLHVVPVGDDAMLNGVLQGQDATLALGLVAHVGVLLAH
AHHDALQGTIRQPRRRHRTHPATQNPGAPRRHPLTWCLGRPTMEGNTARG
ASSPAKPALHMPEPLSMTSAAISSSIATCPEKDGLRRARL
9- LTTPTQEGRLEQRLRTPEPLIANGDDLAIGQLVALLQRRGGCGGGHLLLE
VQGDVAQLLLDVAHDFPLGRGGEAVASLSEDLHEVVGQVPASQVQTQDGV
GEGVALVDGHRVGDPVSRVHDNASGAPRGVEGQHGLDGHVHGRGVEGLKH
NLRRDKGRLSQGQRPTATPCSHATTCCMPV
10- KHLRWTMEGPDSSYSCLLIHICWKVDSEARMEPPIHTEYLRSGGAMICKD
SQARLQLAERPPVSSPEPGRGPPTPRLTLIFMVLGARAVISFCILSAMPG
YMVVPPDSTVLAYRSLRMSTSHFMMELKVVSWMPQDSIPRGQSPPLVMLC
HRG
[Forward Clusters]
Frm Start End Score
2 1053 1445 50
2 1134 1373 9
0 922 1116 3
2 1134 1445 4
0 922 1088 2
0 916 1116 1
0 916 1088 0
Frm Start End Score
0 1651 2148 44
0 1681 2098 33
0 1681 2148 35
0 1651 2098 34
0 1681 2089 31
0 1654 2148 36
0 1744 2098 26
0 1654 2089 32
0 1651 2089 31
0 1744 2089 25
0 1654 2098 32
Frm Start End Score
1 2171 2350 89
1 2171 2419 51
1 2140 2419 14
1 2213 2419 14
1 2140 2350 13
1 2213 2350 10
1 2303 2350 2
1 2279 2350 2
Frm Start End Score
1 2444 2587 75
1 2460 2587 49
1 2522 2587 1
[Reverse Clusters]
Frm Start End Score
1 1019 1462 74
1 1136 1462 15
1 1244 1462 4
Frm Start End Score
1 1499 2023 35
Frm Start End Score
2 2136 2708 74
2 2163 2708 69
0 2434 2637 2
2 2341 2708 1
0 2443 2637 0
Note that each exon, shadow exon, and exon translation have a number
prepended to each line. This number is used to select the feature for
a GenQuest search. Only searchable features have this prepended number.
Guide to GRAIL 1.3 Services
*
Same service for all organisms, Feature\Organism Human Mouse Arabidopsis Drosophila E. coli Options-Params
FtrLabel\OrgLabel
Grail I
grail1exons
3 opts
Grail IA
grail1aexons
3 opts
Grail II
grail2exons
4 opts
Gap2
gap2
3 opts, 3 params
PolyA Sites
polya
1 opt
PolII Promoters
polIIprom
1 opt
CPG Islands*
cpg
1 opt
Repetitive*
rpttv
1 opt, 1 param
Simple Repetitive*
smprpt1 opt
Frame Shift Errors
fserr
1 opt, 1 param
OrgLabel not specified
*
All features have the option Feature Options*
Param-1 Param-2 Param-3
grail1exonsstrandscores
translation
grail1aexonsshadowexons
translation
grail2exonsclusters
shadowexons
translation
gap2genemodel_translation
modelexon_translationAUTO_STRAND
FORWARD_STRAND
REVERSE_STRANDstart
end
polya
polIIprom
cpg
rpttv
OrgLabel
smprpt
fserr
AUTO_STRAND
FORWARD_STRAND
REVERSE_STRAND
header
[Request_FtrLabel_OrgLabel_Version]
[Option= option-1]
...
[Option= option-n]
[Params= param-1 ... param-n]
[Start DNASequence]
ACGTACCGACTCGACTAGCATC...
...
[End DNASequence]
[End_Request]
cpg, rpttv, and smprpt.
gap2 and polIIprom, the
cluster tables returned by grail2exons must be included at
the end of the DNA sequence. For example:
[Request_gap2_arabd_1.3]
[Option= genemodel_translation]
[Option= modelexon_translation]
[Params= AUTO_STRAND 1 3583]
[Start DNASequence]
...
[End DNASequence]
[Start clusters forward]
[Num= 2]
[Start cluster]
1474 1526 1 25 0
[End cluster]
[Start cluster]
2738 2798 1 61 2
2738 2804 1 34 2
[End cluster]
[End clusters forward]
[Start clusters reverse]
[Num= 1]
[Start cluster]
160 317 1 46 0
[End cluster]
[End clusters reverse]
[End_Request]
Last Modified on:
Wed Jul 24 08:22:35 EDT 1996
Refer questions to:
grailmail@ornl.gov