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
--------------------------------------------------------------------------------
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)
--------------------------------------------------------------------------------
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)

--------------------------------------------------------------------------------
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
--------------------------------------------------------------------------------
# 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)
--------------------------------------------------------------------------------
PERCEVAL CpG Islands (0 predicted)

--------------------------------------------------------------------------------
# Output_end: pretty

gc_object_end: cpg_grailexp --output pretty