est2genome.txt

emboss的linux版本的源代码

XX
CC   IMPORTANT:  This sequence is not the entire insert of clone
CC   NFG9.  It may be shorter because we only sequence overlapping
CC   sections once, or longer because we arrange for a small
CC   overlap between neighbouring submissions.
XX
CC   The true left end of clone NFG9 is at 1 in this sequence.
CC   The true left end of clone RA36 is at 25872.
XX
CC   NFG9 is from a 280kb clone contig extending from the telomere of 16p.
CC   Higgs D.R., Flint J. unpublished. MRC Molecular Haematology Unit,
CC   Institute of Molecular Medicine, Oxford.
CC   NFG9 is from the library CV007K. Choo et al.,(1986) Gene 46. 277-286.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..33760
FT                   /chromosome="16"
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /map="16p13.3"
FT                   /clone_lib="CV007K"


  [Part of this file has been deleted for brevity]

     gagacagcag agtgctcagc tcatgaagga ggcaccagcc gccatgcctc tacatccagg     3084
0
     tctcctgggg ttcccacctc cacaaaaacc cccactgcta ggagtgcagg caggagggga     3090
0
     cctgagaacc gacagttata ggtcctgcgg gtgggcagtg ctgggtgttc tggtctgccc     3096
0
     cacccctgtg tgcctagatc cccatctggg cctcaagtgg gtgggattcc aaaggaagag     3102
0
     ccggagtagg cgtggggagg ggcaggccca ggctggacaa agagtctggc cagggagcgg     3108
0
     cacattgccc tcccagagac agtggctcag tgtccaggcc ttccccaggc gcacagtggg     3114
0
     ctcttgttcc cagaaagccc ctcgggggga tccaaacagt gtctccccca ccccgctgac     3120
0
     ccctcagtgt atggggaaac cgtggcccac ggaaggcctc actgcctggg gtcacacagc     3126
0
     atctgagtca ctgcagcagc ctcacagctg ccagcccagg cccagcccca tcaggagaca     3132
0
     cccaaagcca cagtgcatcc caggaccagc tgggggggct gcgggcagga ctctcgatga     3138
0
     ggctgaggga cgaggagggt caagggagcc actggcgcca tgcatgctga cgtcccctct     3144
0
     ggctgcctgc agagcctggt gtggaagggc tgagtggggg atggtggaga gtcctgttaa     3150
0
     ctcaggtttc tgctctgggg atgtctgggc acccatcaag ctggccgcgt gcacaggtgc     3156
0
     agggagagcc agaaagcagg agccgatgca gggaggccac tggggacagc ccaggctgat     3162
0
     gcttgggccc catgtgtctc caccacctac aaccctaagc aagcctcagc tttcccatct     3168
0
     ggaaatcagg ggtcacagca gtgcctggca cagtagcagc ggctgactcc atcacagggt     3174
0
     ggtgtagcct gtgggtactt ggcactctct gaggggcagg agctgggggg tgaaaggacc     3180
0
     ctagagcata tgcaacaaga gggcagccct ggggacacct ggggacagaa ccctccaaag     3186
0
     gtgtcgagtt tgggaagaga ctagagagaa gctctggcca gtccaggcat agacagtggc     3192
0
     cacagccagt ggagagctgc atcctcaggt gtgagcagca accacctctg tactcaggcc     3198
0
     tgccctgcac actcacagga ccatgctggc agggacaact ggcggcggag ttgactgcca     3204
0
     accccggggc cagaaccatc aagcctgggc tctgctccgc ccaaggaact gcctgctgcc     3210
0
     gaggtcagct ggagcaaggg gcctcacccc gggacacctt cccagacgtg tcctcagctc     3216
0
     acatgagcct catcccaggg ggatgtggct cctccagcat ccccacccac acgctgctct     3222
0
     ctgaccctca gtcttctgtt tgactcctaa tctgaagctc aatcctagat ctcccttgag     3228
0
     aagggggtca ccagctgtct ggcagcccag cctccaggtc ttctggatta atgaagggaa     3234
0
     agtcacctgg cctctctgcc ttgtctatta atggcatcat gctgagaatg atatttgcta     3240
0
     ggccctttgc aaaccccaaa gtgctcttca accctcccag tgaagcctct tcttttctgt     3246
0
     ggaagaaatg aggttcaggg tggagcaggg caggcctgag acctttgcag ggttctctcc     3252
0
     aggtccccag caggacagac tggcaccctg cctcccctca tcaccctaga caaggagaca     3258
0
     gaacaagagg ttccctgcta caggccatct gtgagggaag ccgccctagg gcctgtagac     3264
0
     acaggaatcc ctgaggacct gacctgtgag ggtagtgcac aaaggggcca gcacttggca     3270
0
     ggaggggggg gggcactgcc ccaaggctca gctagcaaat gtggcacagg ggtcaccaga     3276
0
     gctaaacccc tgactcagtt gggtctgaca ggggctgaca tggcagacac acccaggaat     3282
0
     caggggacac caagtgcagc tcagggcacc tgtccaggcc acacagtcag aaaggggatg     3288
0
     gcagcaagga cttagctaca ctagattctg ggggtaaact gcctggtatg ctggtcactg     3294
0
     ctagtcccca gtctggagtc tagctgggtc tcaggagtta ggcgaaaaca ccctccccag     3300
0
     gctgcaggtg ggagaggccc acatcccctg cacacgtctg gccagaggac agatgggcag     3306
0
     cccagtcacc agtcagagcc ctccagaggt gtccctgact gaccctacac acatgcaccc     3312
0
     aggtgcccag gcacccttgg gctcagcaac cctgcaaccc cctcccagga cccaccagaa     3318
0
     gcaggatagg actagagagg ccacaggagg gaaaccaagt cagagcagaa atggcttcgg     3324
0
     tcctcagcag cctggctcag cttcctcaaa ccagatcctg actgatcaca ctggtctgtc     3330
0
     taacccctgg gaggggtcct ctgtatccat cttacagata aggaaactga ggctcagaga     3336
0
     agcccatcac tgcctaaggt cccagggcct ataagggagc tcaaagcctt gggccaggtc     3342
0
     tgcccaggag ctgcagtgga agggaccctg tctgcagacc cccagaagac aaggcagacc     3348
0
     acctgggttc ttcagccttg tggctgtgga cggctgtcag acccttctaa gaccccttgc     3354
0
     cacctgctcc atcaggggca tctcagttga agaaggaagg actcaccccc aaaatcgtcc     3360
0
     aactcagaaa aaaaggcaga agccaaggaa tccaatcact gggcaaaatg tgatcctggc     3366
0
     acagacactg aggtggggga actggagccg gtgtggcgga ggccctcaca gccaagagca     3372
0
     actgggggtg ccctgggcag ggactgtagc tgggaagatc                           3376
0
//

Output file format

  Output files for usage example

  File: hs989235.est2genome

Note Best alignment is between forward est and forward genome, but splice sites
 imply REVERSED GENE
Exon       163  91.8 25685 25874 HSNFG9           1   193 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
-Intron    -20   0.0 25875 26278 HSNFG9
Exon       207  98.1 26279 26492 HSNFG9         194   407 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
-Intron    -20   0.0 26493 27390 HSNFG9
Exon        63  86.4 27391 27476 HSNFG9         408   494 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.

Span       393  93.6 25685 27476 HSNFG9           1   494 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.

Segment     14  83.3 25685 25702 HSNFG9           1    18 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
Segment     28  85.7 25703 25737 HSNFG9          20    54 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
Segment      4 100.0 25738 25741 HSNFG9          56    59 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
Segment     13 100.0 25742 25754 HSNFG9          61    73 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
Segment      4 100.0 25756 25759 HSNFG9          74    77 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
Segment    110  97.4 25760 25874 HSNFG9          79   193 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
Segment     37 100.0 26279 26315 HSNFG9         194   230 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
Segment    162  98.8 26317 26480 HSNFG9         231   394 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
Segment     12 100.0 26481 26492 HSNFG9         396   407 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
Segment     16 100.0 27391 27406 HSNFG9         408   423 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
Segment     10  91.7 27407 27418 HSNFG9         425   436 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
Segment     19  95.2 27419 27439 HSNFG9         438   458 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.
Segment     24  80.6 27441 27476 HSNFG9         459   494 HS989235      yo13c02
.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA
sequence.

  MSP type segments

   There are four types of segment,
    1. each gapped Exon
    2. each Intron (marked with a ? if it does not start GT and end AG)
    3. the complete alignment Span
    4. individual ungapped matching Segments.

   The score for Exon segments is the alignment score excluding flanking
   intron penalties. The Span score is the total including the intron
   costs.

   The coordinates of the genomic sequence always refer to the positive
   strand, but are swapped if the est has been reversed. The splice
   direction of Introns are indicated as +Intron (forward, splice sites
   GT/AG) or -Intron (reverse, splice sites CT/AC), or ?Intron (unknown
   direction). Segment entries give the alignment as a series of ungapped
   matching segments.

  Full alignment

   You get the alignment if the -align switch is set. The alignment
   includes the first and last 5 bases of each intron, together with the
   intron width. The direction of splicing is indicated by >>>> (forward)
   or <<<< (reverse) or ???? (unknown)

Data files

   None

Notes

   est2genome uses a linear-space dynamic-programming algorithm. It has
   the following parameters:
parameter               default         description

match                   1               score for matching two bases
mismatch                1               cost for mismatching two bases
gap_penalty             2               cost for deleting a single base in
                                        either sequence,
                                        excluding introns
intron_penalty          40              cost for an intron, independent of
                                        length.
splice_penalty          20              cost for an intron, independent of
                                        length and starting/ending on
                                        donor-acceptor sites.

space                   10              Space threshold (in  megabytes)
                                        for linear-space recursion. If the
                                        product of the two sequence
                                        lengths divided by 4 exceeds this then
                                        a divide-and-conquer strategy is used
                                        to control the memory requirements.
                                        In this way very long sequences can
                                        be aligned.
                                        If you have a machine with plenty of
                                        memory you can raise this parameter
                                        (but do not exceed the machine's
                                        physical RAM)
                                        However, normally you should not need
                                        to change this parameter.

   There is no gap initiation cost for short gaps, just a penalty
   proportional to the length of the gap. Thus the cost of inserting a
   gap of length L in the EST is
 L*gap_penalty

   and the cost in the genome is

min { L*gap_penalty, intron_penalty } or
min { L*gap_penalty, splice_penalty } if the gap starts with GT and ends with A
G
                                     (or CT/AC if splice direction reversed)

   Introns are not allowed in the EST. The difference between the
   intron_penalty and splice_penalty allows for some slack in marking the
   intron end-points. It is often the case that the best intron
   boundaries, from the point of view of minimising mismatches, will not
   coincide exactly with the splice consensus, so provided the difference
   between the intron/splice penalties outweighs the extra mismatch/indel
   costs the alignment will respect the proper boundaries. If the
   alignment still prefers boundaries which don't start and end with the
   splice consensus then this may indicate errors in the sequences.

   The default parameters work well, except for very short exons (length
   less than the splice_penalty, approx) which may be skipped. The intron
   penalties should not be set to less that the maximum expected random
   match between the sequences (typically 10-15 bp) in order to avoid
   spurious matches. The algorithm has the following steps:
    1. A first-pass Smith-Waterman scan is done to locate the score,
       start and end of the maximal scoring segment (including introns of
       course). No other alignment information is retained.
    2. Subsequences corresponding to the maximal-scoring segments are
       extracted. If the product of these subsequences' lengths is less
       than the area parameter then the segments are re-aligned using the
       Needleman-Wunsch algorithm, which in this instance will give the
       same result as the Smith-Waterman since they are guaranteed to
       align end-to-end.
    3. If the product of lengths exceeds the area threshold then the
       alignment is recursively broken down by splitting the EST in half
       and finding the genome position which aligns with the EST
       mid-point. The problem then reduces to aligning the left-hand and
       right-hand portions of the sequences separately and merging the
       result.

   The worst-case run-time for the algorithm is about 3 times as long as
   would be taken to align using a quadratic-space program. In practice
   the maximal-scoring segment is often much shorter than the full genome
   length so the program runs only about 1.5 times slower.

References

    1. Mott R. (1997) EST_GENOME: a program to align spliced DNA
       sequences to unspliced genomic DNA. Comput. Applic. 13:477-478
    2. Huang X (1994) On global sequence alignment. Comput. Applic.
       Biosci. 10:227-235.
    3. Myers, EW and Miller, W (1988) Optimal alignments in linear space.
       Comput. Applic. Biosci. 4:11-17
    4. Smith, TE and Waterman, MS (1981) Identification of common
       molecular subsequences. J. Mol. Biol. 147:195-197

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It returns 0 unless an error occurs.

Known bugs

   None.

See also

   Program name                      Description
   needle       Needleman-Wunsch global alignment
   stretcher    Finds the best global alignment between two sequences

Author(s)

   This application was modified for inclusion in EMBOSS by Peter Rice
   (pmr