gc_object_start: gene_grailexp --organism human --output pretty --dbpat grailexp_v3
# Service: gene_grailexp
# Version: 3.0
# Description: GAT GrailEXP Gene Prediction Service
# Last Modified: December 4, 2000
# Tool: GrailEXP 3.2 from ORNL. Last updated: February, 2001.
# Database: GrailEXP EST/mRNA Database Feb/2001 from NCBI/Baylor/TIGR (7058810 entries). Last updated: February 8, 2001.
# Sequence Name: >gene_grailexp|PID=1704
# Sequence Length: 3864
# Output_begin: pretty
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GrailEXP v3.2 http://compbio.ornl.gov/grailexp/
Authors: Doug Hyatt, Manesh Shah, Victor Olman, Richard Mural, Ying Xu, and
Edward C. Uberbacher, 1996-2001
Reference: "Automated Gene Identification in Large-Scale Genomic Sequences",
Xu, Y. and Uberbacher, E.C., Journal of Computational Biology, Volume 4,
Number 3, 1997
Sequence: >gene_grailexp|PID=1704 (3864 bp)
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GAWAIN Gene Predictions (1 predicted, 1 with database similarity)
Genes with Database Similarity (1 predicted, 0 with alternative splices)
Gene 1, Variant 1 Strand: + Bounds: 1646-3436 Exons: 3
Start Codon: Yes Stop Codon: Yes
Top-Scoring Reference: HT2372 (465 bp) (100% id, 1646-3435)
>human|HT2372|tigr|insulin, 3'
Reference Path: HT2372 (465 bp) (100%, 1646-3435)
AW583755.1 (477 bp) (96%, 1656-3436)
---Index---- --------Exons-------- ---------CDS--------- -Ph- -Fr- -Len- -Scr-
1.1.1 1646 1687 ... ... 1 0 42 100
1.1.2 1867 2070 1884 2070 1 2 204 100
1.1.3 3217 3436 3217 3362 1 2 220 100
PolyA 3416 3421 ... ... . . 6 89
>GrailEXP Gene 1, Var 1 mRNA|Similar to HT2372
agccctccaggacaggctgcatcagaagaggccatcaagcagatcactgtccttctgccatggccctgtg
gatgcgcctcctgcccctgctggcgctgctggccctctggggacctgacccagccgcagcctttgtgaac
caacacctgtgcggctcacacctggtggaagctctctacctagtgtgcggggaacgaggcttcttctaca
cacccaagacccgccgggaggcagaggacctgcaggtggggcaggtggagctgggcgggggccctggtgc
aggcagcctgcagcccttggccctggaggggtccctgcagaagcgtggcattgtggaacaatgctgtacc
agcatctgctccctctaccagctggagaactactgcaactagacgcagcctgcaggcagccccacacccg
ccgcctcctgcaccgagagagatggaataaagcccttgaaccagcc
>GrailEXP Gene 1, Var 1 protein|Derived from similarity to HT2372
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG
GPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN*
Genes with No Database Evidence (0 predicted)
--------------------------------------------------------------------------------
GALAHAD Gene Alignments (94 located: 8 displayed, 86 redundant)
Index Std Begin End Accession Database Organism Length
1 + 1297 2050 C06683.1 dbest other 341
2 pieces Seq exons = (1297..1350,1996..2050)
94% ident Ref exons = (1..59,60..116)
2 + 1646 3435 HT2372 tigr human 465
3 pieces Seq exons = (1646..1687,1867..2070,3217..3435)
100% ident Ref exons = (1..42,43..246,247..465)
3 + 1656 3436 AW583755.1 dbest human 477
3 pieces Seq exons = (1656..1687,1867..2070,3217..3436)
97% ident Ref exons = (1..32,33..236,237..458)
4 + 1665 3433 BE970136.1 dbest human 530
3 pieces Seq exons = (1665..1687,1867..2070,3217..3433)
99% ident Ref exons = (1..23,24..227,228..442)
5 + 1667 3435 AW951286.1 dbest human 581
3 pieces Seq exons = (1667..1687,1867..2070,3217..3435)
99% ident Ref exons = (1..21,22..225,226..444)
6 + 1883 3362 C06636.1 dbest other 484
2 pieces Seq exons = (1883..2070,3217..3362)
82% ident Ref exons = (17..205,206..350)
7 + 1883 3364 AI006503.1 dbest mouse 437
2 pieces Seq exons = (1883..2070,3217..3364)
84% ident Ref exons = (51..239,240..386)
8 + 1981 3436 AW583874.1 dbest human 520
2 pieces Seq exons = (1981..2070,3217..3436)
96% ident Ref exons = (170..264,265..485)
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PERCEVAL Exon Candidates (2 predicted)
Index Std Begin End Frm Type Len Scr Quality
1 + 1867 2070 1 Internal 204 83 Good
2 + 3541 3621 1 Internal 81 52 Marginal
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# Output_end: pretty
gc_object_end: gene_grailexp --organism human --output pretty --dbpat grailexp_v3
gc_object_start: cpg_grailexp --output pretty
# Service: cpg_grailexp
# Version: 3.0
# Description: GAT GrailEXP CpG Island Locator
# Last Modified: December 4, 2000
# Tool: GrailEXP 3.2 from ORNL. Last updated: February, 2001.
# Sequence Name: >cpg_grailexp|PID=17732
# Sequence Length: 3864
# Output_begin: pretty
--------------------------------------------------------------------------------
GrailEXP v3.2 http://compbio.ornl.gov/grailexp/
Authors: Doug Hyatt, Manesh Shah, Victor Olman, Richard Mural, Ying Xu, and
Edward C. Uberbacher, 1996-2001
Reference: "Automated Gene Identification in Large-Scale Genomic Sequences",
Xu, Y. and Uberbacher, E.C., Journal of Computational Biology, Volume 4,
Number 3, 1997
Sequence: >cpg_grailexp|PID=17732 (3864 bp)
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PERCEVAL CpG Islands (0 predicted)
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# Output_end: pretty
gc_object_end: cpg_grailexp --output pretty