Need your help for XDAP in STADEN

Qingquan Fang qfang at GLUE.UMD.EDU
Sun Aug 13 15:08:40 EST 1995


Hi Netters,

I encounted problems when assumbling contigues using XDAP in STADEN.

Here is the output messages.  Could somebody tell me what's the problems?

 DAP (Development assembly program) V5.1 Aug 1992
 Author: Rodger Staden
Maximum set to  1024
 Writing new database files
 Database AFA-V03 version 0, size   50 successfully started
 Automatic sequence assembler
 Database is logically consistent
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Processing  1 in batch
 Gel reading name=Afav03-17f4dSW3                         
 Gel reading length=   402
 New gel reading does not overlap: start a new contig
 This gel reading has been given the number      1

 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Processing  2 in batch
 Gel reading name=Afav03-4dr17SW3                         
 Gel reading length=   367
 Contig    1 position   351 matches strand 2 at position   32
Total matches found  1
Trying to align with contig  1
 Padding in contig=    3 and in gel=    4
 Percentage mismatch after alignment = 11.9
 Best alignment found
322        332        342        352        362        372
  AAACCCTGTC AGGAGGC,AA TC,G,AAGAA GTTATTCGCA ATGGGACTTG ATTCCATTCT
  ******** * ******* ** ** * ***** * ******** **** ** ** **********
  AAACCCTG,C AGGAGGCCAA TCCGAaAGAA GATATTCGCA ATGG,AC,TG ATTCCATTCT
  1          11         21         31         41         51
382        392        402
  ACGTCGTGGC TACTTTTGGG TTAC
  ********** ****** *** *  *
  ACGTCGTGGC TACTTT,GGG TACC
 61         71         81
 New gel reading overlaps contig     1
 This gel reading has been given the number      2
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Processing  3 in batch
 Gel reading name=Afav03-17f32SW3                         
 Gel reading length=   478
 Contig    1 position    11 matches strand 1 at position   30
 Contig    1 position   459 matches strand 1 at position  466
Total matches found  2
Trying to align with contig  1
 Padding in contig=    2 and in gel=   15
 Percentage mismatch after alignment =  6.3
 Best alignment found
  1         11         21         31         41         51
  GAAGTAGTAG ATGTTGGACT GGCTGGGCAG ACTGCTTGGC CTGCCCGAGT CGTTCCTGGC
  *********  ********** ********** *   ****** ********** **********
  GAAGTAGTA, ATGTTGGACT GGCTGGGCAG AT-,CTTGGC CTGCCCGAGT CGTTCCTGGC
 21         31         41         51         61         71

 61         71         81         91        101        111
  CCGTCCGGGA GGCGAGGCCG GCGGTGTCAT CCAAGGCACC GCCAGCAAGG CTACGTTGGT
  ********** ********** **** ***** ********** ********** **********
  CCGTcCGGGa GGCGAGGCCG gCGGCGTCAT CCAAGGCACC GCCAGCAAGG CTACGTTGGT
 81         91        101        111        121        131

......

Trying to align with contig  1
 Padding in contig=    2 and in gel=   15
 Percentage mismatch after alignment =  6.3
 Best alignment found
  1         11         21         31         41         51
  GAAGTAGTAG ATGTTGGACT GGCTGGGCAG ACTGCTTGGC CTGCCCGAGT CGTTCCTGGC
  *********  ********** ********** *   ****** ********** **********
  GAAGTAGTA, ATGTTGGACT GGCTGGGCAG AT-,CTTGGC CTGCCCGAGT CGTTCCTGGC
 21         31         41         51         61         71

......

 Overlap between contigs     1 and     1
 Trying to form loop in contig  1
 Gel not entered
 Failed gel name written to error file
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Processing  4 in batch
 Gel reading name=Afav03-32r17SW3                         
 Gel reading length=   489
 Contig    1 position    10 matches strand 2 at position   38
 Contig    1 position   461 matches strand 2 at position  477
Total matches found  2
Trying to align with contig  1
 Padding in contig=    2 and in gel=   14
 Percentage mismatch after alignment =  5.7
 Best alignment found
  1         11         21         31         41         51
  GAAGTA,GTA GATGTTGGAC TGGCTGGGC, AGACTGCTTG GCCTGCCCGA GTCGTTCCTG
  ****** **  ********** *********  *** ****** ********** **********
  GAAgTAAgT, gATGTTGGAC TGGCTGGGCC AGA,TgCTTG GCCTgCCCGA GTCGTTCCTG
 29         39         49         59         69         79
 61         71         81         91        101        111
  GCCCGTCCGG GAGGCGAGGC CGGCGGTGTC ATCCAAGGCA CCGCCAGCAA GGCTACGTTG
  ****** *** ********** ****** *** ********** ****** * * **********
  GCCCGTTCGG GAGGCgAGGC CGGCGGCGTC ATCCAAGGCA CCGCCA-CGA GGCTACGTTG
 89         99        109        119        129        139

......

Trying to align with contig  1
 Padding in contig=    2 and in gel=   14
 Percentage mismatch after alignment =  5.7
 Best alignment found
  1         11         21         31         41         51
  GAAGTA,GTA GATGTTGGAC TGGCTGGGC, AGACTGCTTG GCCTGCCCGA GTCGTTCCTG
  ****** **  ********** *********  *** ****** ********** **********
  GAAgTAAgT, gATGTTGGAC TGGCTGGGCC AGA,TgCTTG GCCTgCCCGA GTCGTTCCTG
 29         39         49         59         69         79
 61         71         81         91        101        111
  GCCCGTCCGG GAGGCGAGGC CGGCGGTGTC ATCCAAGGCA CCGCCAGCAA GGCTACGTTG
  ****** *** ********** ****** *** ********** ****** * * **********
  GCCCGTTCGG GAGGCgAGGC CGGCGGCGTC ATCCAAGGCA CCGCCA-CGA GGCTACGTTG
 89         99        109        119        129        139
121        131        141        151        161        171

......

 Overlap between contigs     1 and     1
 Trying to form loop in contig  1
 Gel not entered
 Failed gel name written to error file
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
    .

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 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Processing  12 in batch
 Gel reading name=Afav03-32f4dSW2                         
 Gel reading length=   209
 Contig    1 position   503 matches strand 1 at position    9
Total matches found  1
Trying to align with contig  1
 Padding in contig=    0 and in gel=    0
 Percentage mismatch after alignment =  1.4
 Best alignment found
495        505        515        525        535        545
  TGGATCC-GC ATTCATCTGT CCTGAGTACC -GGTACCTTA TGAAGGGCGT CGAGAAAGCA
  ******* ** ********** **********  ********* ********** **********
  TGGAtcCTGC ATTCAtCTGT CCTGAGTACC TGGTACCTTA TGAAGGGCGT CGAGAAAGCA
  1         11         21         31         41         51
555        565        575        585        595        605
  AGTTCCTTCA ACTTAAATCC TCACAAATGG TTATTAGTCA ACTTTGACTG T-CCGCCTTG
  ********** ********** ********** ********** ********** * ********
  AGTTCCTTCA ACTTAAATCC TCACAAATGG TTATtAGTCA ACTTTgACTG TtCCGCCTTG

 New gel reading overlaps contig     1
 New gel already in database with number     3 Entry aborted
 Failed gel name written to error file
Batch finished
  12 sequences processed
  3 sequences entered into database
  0 joins made
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

QUESTIONS:

1)  There is good homology between the contigs, why is only 3 of 12 
	assumbled?

2)  There was a error message:

    " Overlap between contigs     1 and     1
      Trying to form loop in contig  1
      Gel not entered
      Failed gel name written to error file"

   What did cause the "Gel not entered"?  Is the gel file name (15 
        letters) to long? 

3) What does this error message mean, "New gel already in database with
        number 3.  Entry aborted."?  
        The two gels have different file nambes. 

4) How to make the assumbling program working in my case?

Your help will be greatly appreciated.

 +==================================================+
 |   Qingquan Fang, Ph.D.                           |
 |   Postdoctoral Research Associate                |
 |   Center for Agricultural Biotechnology (CAB)    |
 |   2113 Agriculture/Life Sciences Surge Bldg.     |
 |   University of Maryland                         |
 |   College Park, MD 20742-3351                    |
 |        --------------------------------          |
 | Phone: (301)-405-6937       Fax: (301)-314-9075  |
 | Internet: qfang at wam.umd.edu / qfang at glue.umd.edu |
 +==================================================+




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