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\OT1/ptm/m/n/10.95 The core DP al-go-rithms have been ex-tended by the \OT1/ptm
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\OT1/ptm/m/n/10.95 ally 1), if their cov-er-age is higher than the ar-gu-ment [
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\OT1/ptm/m/n/10.95 With the help of \OT1/pcr/m/n/10.95 gthgetseq \OT1/ptm/m/n/1
0.95 one can get the used \OT1/ptm/m/sc/10.95 Fasta \OT1/ptm/m/n/10.95 se-quenc
es from \OT1/ptm/m/it/10.95 Genome-
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[]\OT1/ptm/m/n/10.95 At least one of the op-tions [], [], [], [],
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inter.gz 
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inter.gz > cdna 
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\OT1/pcr/m/n/10.95 gthfilestat \OT1/ptm/m/n/10.95 shows statis-tics about splic
ed align-ments in \OT1/ptm/m/it/10.95 Genome-Threader \OT1/ptm/m/n/10.95 out-
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\OT1/ptm/m/n/10.95 put files con-tain-ing in-ter-me-di-ate re-sults. This might
 be help-ful in get-ting an overview
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[]\OT1/pcr/m/n/8 $ gth -genomic U89959_genomic.fas -cdna U89959_ests.fas -gff3o
ut -skipalignmentout -md5ids 
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[]\OT1/pcr/m/n/8 $ gthbssmbuild -gtdonor -agacceptor -datapath training_data -b
ssmfile arab.bssm 
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\OT1/ptm/m/n/10.95 con-tain-ing the train-ing data. The train-ing data is usu-a
lly gen-er-ated with \OT1/pcr/m/n/10.95 gthbssmtrain
 []

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No file ../scripts/gthclean.sh.
[33] [34]
File: output/gth--genomic-NC_003070.fna.gz--cdna-AU236313.gbk.gz.out  (verbatim
)

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[]\OT1/pcr/m/n/8 **************************************************************
******************[] 
 []


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[]\OT1/pcr/m/n/8 EST Sequence: file=AU236313.gbk.gz, strand=+, description=AU23
6313 AU236313 RAFL14 Arabidopsis thaliana cDNA clone RAFL14-87-E12 5',[] 
 []


Overfull \hbox (446.40051pt too wide) in paragraph at lines 1287--1287
[]\OT1/pcr/m/n/8 Genomic Template: file=NC_003070.fna.gz, strand=+, from=382240
, to=383395, description=gi|42592260|ref|NC_003070.5| Arabidopsis thaliana chro
mosome 1, complete sequence[] 
 []


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[] \OT1/pcr/m/n/8 Exon  1   382540   382567 (  28 n);  cDNA      1     28 (  28
 n); score: 1.000[] 
 []


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[]  \OT1/pcr/m/n/8 Intron  1   382568   382802 ( 235 n); Pd: 0.050 (s:    0), P
a: 0.050 (s: 0.95)[] 
 []


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[] \OT1/pcr/m/n/8 Exon  2   382803   382929 ( 127 n);  cDNA     29    156 ( 128
 n); score: 0.980[] 
 []


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[]  \OT1/pcr/m/n/8 Intron  2   382930   383029 ( 100 n); Pd: 0.050 (s: 1.00), P
a: 0.050 (s: 1.00)[] 
 []


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[] \OT1/pcr/m/n/8 Exon  3   383030   383100 (  71 n);  cDNA    157    227 (  71
 n); score: 0.944[] 
 []


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[]\OT1/pcr/m/n/8 GCGTGTTGTT AAAGAGCTCA CTAGTTGGGT ATGTTTACAA CCTTTTCAAG ATTTCAC
TTC      382599[] 
 []


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[]\OT1/pcr/m/n/8 GCGTGTTGTT AAAGAGCTCA CTAGTTGG.. .......... .......... .......
...          28[] 
 []


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[]\OT1/pcr/m/n/8 GCTGATGTGC TTTGTTCAGT TACTTCTCCA TTAATTTGTC ACTATTTCTG TCAGAAC
ACA      382659[] 
 []


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[]\OT1/pcr/m/n/8 .......... .......... .......... .......... .......... .......
...          28[] 
 []


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[]\OT1/pcr/m/n/8 TAGGATAACA CATATCATAT AAGTGCTAGG TCGAGTCTGT TTCCTGTAGT TGGAGCC
TAT      382719[] 
 []


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[]\OT1/pcr/m/n/8 .......... .......... .......... .......... .......... .......
...          28[] 
 []


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[]\OT1/pcr/m/n/8 CCTCAACTGG TTATAGATAC TAGATTTGTT TCTTTGGTAT TTTTAGTTAT AATTAAT
TAT      382779[] 
 []


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[]\OT1/pcr/m/n/8 .......... .......... .......... .......... .......... .......
...          28[] 
 []


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[]\OT1/pcr/m/n/8 CTTTCTTCAA ACTTTTGACA CAGGTGATTT ATTCAGAGGA GGAT-CGGAA GCTCAAC
AAA      382838[] 
 []


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[]\OT1/pcr/m/n/8 .......... .......... ...GTGATTT ATTCAGAGGA GGATCCGGAA GCTCAAC
AAA          65[] 
 []

[35]
Overfull \hbox (9.60023pt too wide) in paragraph at lines 1287--1287
[]\OT1/pcr/m/n/8 GATATTACTA TTGGTCTTAT CCAGCGTGAG TTGCTTAGCC TAGCGGAGTA CAATGTC
CAC      382898[] 
 []


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[]\OT1/pcr/m/n/8 GATATTACTA TTGGTCTTAT CCAGCGTGAG TTGCTTAGCC TAGCGGAGTA CAATGTC
CAC         125[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1287--1287
[]\OT1/pcr/m/n/8 ATGGCGAAGC ATCTTGATGG AGGGAGAAAC AGTATGCTGA ATTGCTTAAC CTTTGTT
GAT      382958[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1287--1287
[]\OT1/pcr/m/n/8 ATGGCGAAGC ATCTTGATGG AGGGAGAAAC A......... .......... .......
...         156[] 
 []


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[]\OT1/pcr/m/n/8 GTCCTTGTGT GGTAACATTC TTTTTTTGTT TTGGCTAGTG AACTTGTTTT AACAAGT
TGT      383018[] 
 []


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[]\OT1/pcr/m/n/8 .......... .......... .......... .......... .......... .......
...         156[] 
 []


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[]\OT1/pcr/m/n/8 TTGTTACGCA GAGACCGCAA CTGACTTTGC TATTTCTCTA CTCCAATCCT TGGTCAC
TGA      383078[] 
 []


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[]\OT1/pcr/m/n/8 .......... .AGACCGCAA CTGACTTTGC TATTTCTCTA CTCCAATCCT TGGTCAC
TGA         205[] 
 []


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[]\OT1/pcr/m/n/8 GGAGTCGAGT GTCATTTCAG AG                                      
         383100[] 
 []


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[]\OT1/pcr/m/n/8 GGAGTCNAGT GTCATTTNNT AG                                      
            227[] 
 []


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[]\OT1/pcr/m/n/8 --------------------------------------------------------------
------------------[] 
 []

[36]
File: output/gth--species-arabidopsis--genomic-NC_003070.fna.gz--cdna-AU236313.
gbk.gz--v.out  (verbatim)

Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 $ gth -species arabidopsis -genomic NC_003070.fna.gz -cdna AU2
36313.gbk.gz -v 
 []


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[]\OT1/pcr/m/n/8 $ Arguments: -species arabidopsis -genomic NC_003070.fna.gz -c
dna AU236313.gbk.gz -v[] 
 []

[37]
Overfull \hbox (273.6004pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 # args=-d -v -l 20 -seedlength 18 -exdrop 2 -q AU236313.gbk.gz
.dna /Users/gordon/work/genometools/doc/gthmanual/NC_003070.fna.gz.dna[] 
 []


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[]\OT1/pcr/m/n/8 $ alphabet "aAcCgGtTuUnsywrkvbdhmNSYWRKVBDHM" (size 32) mapped
 to "acgtn" (size 5)[] 
 []


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[]\OT1/pcr/m/n/8 $ alphabet "aAcCgGtTuUnsywrkvbdhmNSYWRKVBDHM" (size 32) mapped
 to "acgtn" (size 5)[] 
 []


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[]\OT1/pcr/m/n/8 # d = distance value (negative=hamming distance, 0=exact, posi
tive=edit distance)[] 
 []


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[]\OT1/pcr/m/n/8 $ overall space peak: main=58.05 MB (2.00 bytes/symbol), secon
dary=214.19 MB (7.38 bytes/symbol)[] 
 []


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[]\OT1/pcr/m/n/8 # args=-p -v -l 20 -seedlength 18 -exdrop 2 -q AU236313.gbk.gz
.dna /Users/gordon/work/genometools/doc/gthmanual/NC_003070.fna.gz.dna[] 
 []


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[]\OT1/pcr/m/n/8 $ alphabet "aAcCgGtTuUnsywrkvbdhmNSYWRKVBDHM" (size 32) mapped
 to "acgtn" (size 5)[] 
 []


Overfull \hbox (33.60025pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 $ alphabet "aAcCgGtTuUnsywrkvbdhmNSYWRKVBDHM" (size 32) mapped
 to "acgtn" (size 5)[] 
 []

[38]
Overfull \hbox (28.80025pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 # d = distance value (negative=hamming distance, 0=exact, posi
tive=edit distance)[] 
 []


Overfull \hbox (100.8003pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 $ overall space peak: main=58.06 MB (2.00 bytes/symbol), secon
dary=214.19 MB (7.38 bytes/symbol)[] 
 []


Overfull \hbox (24.00024pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 **************************************************************
******************[] 
 []


Overfull \hbox (273.6004pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 EST Sequence: file=AU236313.gbk.gz, strand=+, description=AU23
6313 AU236313 RAFL14 Arabidopsis thaliana cDNA clone RAFL14-87-E12 5',[] 
 []


Overfull \hbox (446.40051pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 Genomic Template: file=NC_003070.fna.gz, strand=+, from=382240
, to=383395, description=gi|42592260|ref|NC_003070.5| Arabidopsis thaliana chro
mosome 1, complete sequence[] 
 []


Overfull \hbox (19.20024pt too wide) in paragraph at lines 1296--1296
[] \OT1/pcr/m/n/8 Exon  1   382540   382567 (  28 n);  cDNA      1     28 (  28
 n); score: 1.000[] 
 []


Overfull \hbox (24.00024pt too wide) in paragraph at lines 1296--1296
[]  \OT1/pcr/m/n/8 Intron  1   382568   382802 ( 235 n); Pd: 0.985 (s:    0), P
a: 0.999 (s: 0.95)[] 
 []


Overfull \hbox (19.20024pt too wide) in paragraph at lines 1296--1296
[] \OT1/pcr/m/n/8 Exon  2   382803   382929 ( 127 n);  cDNA     29    156 ( 128
 n); score: 0.980[] 
 []


Overfull \hbox (24.00024pt too wide) in paragraph at lines 1296--1296
[]  \OT1/pcr/m/n/8 Intron  2   382930   383029 ( 100 n); Pd: 0.956 (s: 1.00), P
a: 0.983 (s: 1.00)[] 
 []


Overfull \hbox (19.20024pt too wide) in paragraph at lines 1296--1296
[] \OT1/pcr/m/n/8 Exon  3   383030   383100 (  71 n);  cDNA    157    227 (  71
 n); score: 0.944[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 GCGTGTTGTT AAAGAGCTCA CTAGTTGGGT ATGTTTACAA CCTTTTCAAG ATTTCAC
TTC      382599[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 GCGTGTTGTT AAAGAGCTCA CTAGTTGG.. .......... .......... .......
...          28[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 GCTGATGTGC TTTGTTCAGT TACTTCTCCA TTAATTTGTC ACTATTTCTG TCAGAAC
ACA      382659[] 
 []


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[]\OT1/pcr/m/n/8 .......... .......... .......... .......... .......... .......
...          28[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 TAGGATAACA CATATCATAT AAGTGCTAGG TCGAGTCTGT TTCCTGTAGT TGGAGCC
TAT      382719[] 
 []


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[]\OT1/pcr/m/n/8 .......... .......... .......... .......... .......... .......
...          28[] 
 []


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[]\OT1/pcr/m/n/8 CCTCAACTGG TTATAGATAC TAGATTTGTT TCTTTGGTAT TTTTAGTTAT AATTAAT
TAT      382779[] 
 []


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[]\OT1/pcr/m/n/8 .......... .......... .......... .......... .......... .......
...          28[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 CTTTCTTCAA ACTTTTGACA CAGGTGATTT ATTCAGAGGA GGAT-CGGAA GCTCAAC
AAA      382838[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 .......... .......... ...GTGATTT ATTCAGAGGA GGATCCGGAA GCTCAAC
AAA          65[] 
 []

[39]
Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 GATATTACTA TTGGTCTTAT CCAGCGTGAG TTGCTTAGCC TAGCGGAGTA CAATGTC
CAC      382898[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 GATATTACTA TTGGTCTTAT CCAGCGTGAG TTGCTTAGCC TAGCGGAGTA CAATGTC
CAC         125[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 ATGGCGAAGC ATCTTGATGG AGGGAGAAAC AGTATGCTGA ATTGCTTAAC CTTTGTT
GAT      382958[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 ATGGCGAAGC ATCTTGATGG AGGGAGAAAC A......... .......... .......
...         156[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 GTCCTTGTGT GGTAACATTC TTTTTTTGTT TTGGCTAGTG AACTTGTTTT AACAAGT
TGT      383018[] 
 []


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[]\OT1/pcr/m/n/8 .......... .......... .......... .......... .......... .......
...         156[] 
 []


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[]\OT1/pcr/m/n/8 TTGTTACGCA GAGACCGCAA CTGACTTTGC TATTTCTCTA CTCCAATCCT TGGTCAC
TGA      383078[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 .......... .AGACCGCAA CTGACTTTGC TATTTCTCTA CTCCAATCCT TGGTCAC
TGA         205[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 GGAGTCGAGT GTCATTTCAG AG                                      
         383100[] 
 []


Overfull \hbox (9.60023pt too wide) in paragraph at lines 1296--1296
[]\OT1/pcr/m/n/8 GGAGTCNAGT GTCATTTNNT AG                                      
            227[] 
 []


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[]\OT1/pcr/m/n/8 --------------------------------------------------------------
------------------[] 
 []

[40]
File: output/gth--v--frompos-1--topos-200000--inverse--force--o-arab_mapping.tx
t--cdna-CeresTigr.gz--species-arabidopsis--genomic-NC_003070.fna.gz.out  (verba
tim)

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[]\OT1/pcr/m/n/8 $ gth -v -frompos 1 -topos 200000 -inverse -force -o arab_mapp
ing.txt -cdna CeresTigr.gz -species arabidopsis -genomic NC_003070.fna.gz 
 []

[41]
File: output/gth--species-human--genomic-hs_ref_chr21.fa.gz--cdna-NM_003253.gbk
.out  (verbatim)

Overfull \hbox (7.19958pt too wide) in paragraph at lines 1318--1318
[]\OT1/pcr/m/n/9 $ gth -species human -genomic hs_ref_chr21.fa.gz -cdna NM_0032
53.gbk 
 []

File: output/gth--introncutout--introndistri--species-human--genomic-hs_ref_chr
21.fa.gz--cdna-NM_003253.gbk.out  (verbatim)

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[]\OT1/pcr/m/n/8 $ gth -introncutout -introndistri -species human -genomic hs_r
ef_chr21.fa.gz -cdna NM_003253.gbk 
 []

[42]
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\OT1/ptm/m/n/10.95 align-ments and only re-com-pute the \OT1/ptm/m/it/10.95 con
-sen-sus spliced align-ments \OT1/ptm/m/n/10.95 us-ing \OT1/pcr/m/n/10.95 gthco
nsensus\OT1/ptm/m/n/10.95 . 
 []

File: output/gth--intermediate--xmlout--gzip--o-ceres.inter.gz--genomic-NC_0030
70.fna.gz--cdna-CeresTigr.gz--frompos-300000--topos-500000--inverse.out  (verba
tim)

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[]\OT1/pcr/m/n/8 $ gth -intermediate -xmlout -gzip -o ceres.inter.gz -genomic N
C_003070.fna.gz -cdna CeresTigr.gz -frompos 300000 -topos 500000 -inverse 
 []


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[]\OT1/ptm/m/n/10.95 To look at the re-sults stored in the file \OT1/pcr/m/n/10
.95 ceres.inter.gz\OT1/ptm/m/n/10.95 , we em-ploy \OT1/pcr/m/n/10.95 gthconsens
us
 []

File: output/gthconsensus-ceres.inter.gz.out  (verbatim)

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[]\OT1/pcr/m/n/8 PGS_42592260+_24737-(319898  320145,320252  320296,320380  320
457,320769  321417,321745  321865,321958  322406,322513  322843)[] 
 []


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[]\OT1/pcr/m/n/8 PGS_42592260-_40042+ (389646  389410,389301  389226,389138  38
9050,388940  388851,388760  388716,388609  388539,388406  388268,387672  387584
,387503  387278)[] 
 []

File: output/gthfilestat-ceres.inter.gz.out  (verbatim)
[43]
File: output/gth--intermediate--xmlout--gzip--o-new.inter.gz--genomic-NC_003070
.fna.gz--cdna-AU236313.gbk.gz--frompos-300000--topos-500000--inverse.out  (verb
atim)

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[]\OT1/pcr/m/n/8 $ gth -intermediate -xmlout -gzip -o new.inter.gz -genomic NC_
003070.fna.gz -cdna AU236313.gbk.gz -frompos 300000 -topos 500000 -inverse 
 []

File: output/gthconsensus-ceres.inter.gz-new.inter.gz.out  (verbatim)

Overfull \hbox (244.80038pt too wide) in paragraph at lines 1364--1364
[]\OT1/pcr/m/n/8 PGS_42592260+_24737-(319898  320145,320252  320296,320380  320
457,320769  321417,321745  321865,321958  322406,322513  322843)[] 
 []


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[]\OT1/pcr/m/n/8 PGS_42592260-_40042+ (389646  389410,389301  389226,389138  38
9050,388940  388851,388760  388716,388609  388539,388406  388268,387672  387584
,387503  387278)[] 
 []

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 []\OT1/ptm/b/it/10.95 Genome-Threader \OT1/pcr/b/n/10.95 1.0.0 (2007-06-20)\OT
1/ptm/b/n/10.95 :[] \OT1/ptm/m/n/10.95 Many in-ter-nal changes due to switch
 []


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 []\OT1/ptm/b/it/10.95 Genome-Threader \OT1/pcr/b/n/10.95 0.9.59 (2007-02-08)\O
T1/ptm/b/n/10.95 :[] \OT1/ptm/m/n/10.95 The de-fault value for op-tion []
 []

[44]
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 []\OT1/ptm/b/it/10.95 Genome-Threader \OT1/pcr/b/n/10.95 0.9.57 (2006-09-19)\O
T1/ptm/b/n/10.95 :[] \OT1/ptm/m/n/10.95 The op-tions []
 []


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 []\OT1/ptm/b/it/10.95 Genome-Threader \OT1/pcr/b/n/10.95 0.9.53 (2006-05-23)\O
T1/ptm/b/n/10.95 :[] \OT1/pcr/m/n/10.95 gthbssmbuild \OT1/ptm/m/n/10.95 per-for
ms more
 []


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 []\OT1/ptm/b/it/10.95 Genome-Threader \OT1/pcr/b/n/10.95 0.9.52 (2006-05-22)\O
T1/ptm/b/n/10.95 :[] \OT1/ptm/m/n/10.95 The op-tion []
 []


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 []\OT1/ptm/b/it/10.95 Genome-Threader \OT1/pcr/b/n/10.95 0.9.51 (2006-05-16)\O
T1/ptm/b/n/10.95 :[] \OT1/ptm/m/n/10.95 The plain pro-tein out-put has been
 []


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 []\OT1/ptm/b/it/10.95 Genome-Threader \OT1/pcr/b/n/10.95 0.9.50 (2006-05-14)\O
T1/ptm/b/n/10.95 :[] \OT1/ptm/m/n/10.95 A mi-nor prob-lem con-cern-ing the
 []

[45]
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 []\OT1/ptm/b/it/10.95 Genome-Threader \OT1/pcr/b/n/10.95 0.9.41 (2005-09-21)\O
T1/ptm/b/n/10.95 :[] \OT1/ptm/m/n/10.95 Com-pu-ta-tion of par-al-o-gous genes
 []


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 []\OT1/ptm/b/it/10.95 Genome-Threader \OT1/pcr/b/n/10.95 0.9.40 (2005-09-15)\O
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\OT1/ptm/m/n/10.95 re-placed by the op-tions [] and []. The tools \OT1/pcr/m/n/
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.95 :[] \OT1/ptm/m/n/10.95 The \OT1/pcr/m/n/10.95 gthconsensus \OT1/ptm/m/n/10.
95 pro-gram has been in-tro-duced. 
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95 :[] \OT1/ptm/m/n/10.95 The fol-low-ing op-tions have been in-tro-duced: [],
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