[Bioperl-guts-l] bioperl-live/t/data glimmer3-fragment.detail, NONE, 1.1 glimmer3-fragment.predict, NONE, 1.1

Christopher John Fields cjfields at dev.open-bio.org
Sun Jul 1 18:02:38 EDT 2007


Update of /home/repository/bioperl/bioperl-live/t/data
In directory dev.open-bio.org:/tmp/cvs-serv14313

Added Files:
	glimmer3-fragment.detail glimmer3-fragment.predict 
Log Message:
bug 2299

--- NEW FILE: glimmer3-fragment.predict ---
>gi|123977258|gb|AAVN02000021.1| Collinsella aerofaciens ATCC 25986 C_aerofaciens-2.0_Cont1.6, whole genome shotgun sequence
orf00001        0      674  +3     6.98
orf00002     1071     1253  +3     4.94
orf00003     1231     2511  +1    11.93
orf00005     2677     2934  +1     5.63

--- NEW FILE: glimmer3-fragment.detail ---
Command:  glimmer3 -l -X AAVN02000021.1.fasta aavn.icm glimmer3-fragment

Sequence file = AAVN02000021.1.fasta
Number of sequences = 1
ICM model file = aavn.icm
Excluded regions file = none
List of orfs file = none
Input is NOT separate orfs
Independent (non-coding) scores are used
Circular genome = false
Truncated orfs = true
Minimum gene length = 100 bp
Maximum overlap bases = 30
Threshold score = 30
Use first start codon = false
Start codons = atg,gtg,ttg
Start probs = 0.600,0.300,0.100
Stop codons = taa,tag,tga
GC percentage = 53.3%
Ignore score on orfs longer than 812


>gi|123977258|gb|AAVN02000021.1| Collinsella aerofaciens ATCC 25986 C_aerofaciens-2.0_Cont1.6, whole genome shotgun sequence
Sequence length = 2932

           ----- Start -----           --- Length ----  ------------- Scores -------------
 ID  Frame   of Orf  of Gene     Stop   of Orf of Gene      Raw InFrm F1 F2 F3 R1 R2 R3 NC
        +1       -2       79      192      189     111    -5.50     0  0  - 99  -  -  0  0
        -1      333      270      154      177     114   -13.99     0  -  0 99  0  -  0  0
        -2      340      328      221      117     105    -9.96     0  -  0 93  0  0  1  5
        +2      134      263      424      288     159   -10.03     0  0  0 99  -  -  0  0
        -3      458      233        3      453     228     1.15     0  -  - 99  -  -  0  0
        +1      229      277      540      309     261    -9.76     0  0  - 99  -  -  -  0
0001    +3        0        0      674      669     669     7.01    99  -  - 99  -  -  -  0
        -2      727      580      368      357     210    -3.05     0  -  - 99  -  0  -  0
        -1      786      771      658      126     111   -14.03     0  -  -  -  0  -  - 99
        -2      904      859      728      174     129   -12.38     0  1  -  -  -  0  - 98
        -3      914      905      750      162     153    -0.96    17  0  -  9  -  0 17 72
        +1      718      778      930      210     150    -3.84     0  0  -  1  -  -  - 98
        -1      978      918      787      189     129   -12.66     0  0  -  1  0  - 80 17
        +3      750      804      986      234     180    -4.06     0  -  -  0  -  -  - 99
        -1     1110     1089      979      129     108   -11.01     0  -  0  -  0  -  - 99
        +2      983     1016     1234      249     216    -6.83     0  -  0 96  -  0  -  3
0002    +3     1005     1071     1253      246     180     5.32    99  -  - 99  -  0  -  0
        -2     1339     1225     1013      324     210    -6.58     0  -  0 49  -  0  - 50
        +2     1322     1388     1492      168     102    -8.80     0 99  0  -  0  -  0  0
        -3     1514     1514     1302      210     210    -4.98     0 99  -  -  0  -  0  0
        -1     1605     1221     1111      492     108   -14.08     0  -  0 99  0  0  0  0
        -2     1771     1744     1619      150     123   -16.35     0 99  -  -  0  0  0  0
        +2     1814     1820     1930      114     108    -7.50     0 99  0  -  -  -  0  0
        -3     1973     1622     1515      456     105    -1.02     0 99  0  -  -  -  0  0
        -3     2258     2090     1974      282     114    -5.13     0 99  -  -  0  -  0  0
        +2     2000     2081     2287      285     204   -14.54     0 99  0  -  0  0  -  0
        -2     2335     2332     2018      315     312   -12.59     0 99  -  -  0  0  -  0
        -1     2340     2247     1891      447     354    -3.45     0 99  -  -  0  -  -  0
0003    +1     1177     1231     2511     1332    1278    12.08    99 99  -  -  -  -  -  0
        +2     2288     2453     2560      270     105    -9.51     0  -  0  0  0  -  - 99
        -1     2562     2502     2341      219     159    -1.23     0 99  0  -  0  -  -  0
        +3     2457     2478     2594      135     114   -12.83     0  -  -  0  -  -  - 99
        -3     2831     2816     2652      177     162    -9.05     0 84  -  -  -  -  0 15
        -2     2935     2935     2813      117     117    -9.81     0 99  0  0  0  0  -  0
0004    -1     2934     2880     2755      174     123     2.72    40 25 32  - 40  -  -  1
        +3     2802     2805     2933      129     126    -8.60     0 99  0  0  0  -  -  0
0005    +1     2656     2677     2934      276     255     5.90    99 99  -  -  -  -  -  0
        +2     2699     2798     2935      234     135    -3.20     0 99  0  0  0  -  -  0



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