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Received: (qfang at localhost) by phelix.umd.edu (8.6.10/8.6.4) id PAA09743; Sun, 13 Aug 1995 15:18:04 -0400
Date: Sun, 13 Aug 1995 15:18:01 -0400 (EDT)
From: Qingquan Fang <qfang at Glue.umd.edu>
X-Sender: qfang at phelix.umd.edu
To: software Staden <bionet.software.staden at net.bio.net>
Subject: Need your help
Message-ID: <Pine.SUN.3.91.950813142747.9730A-100000 at phelix.umd.edu>
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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
61 71 81 91 101 111
CCGTCCGGGA GGCGAGGCCG GCGGTGTCAT CCAAGGCACC GCCAGCAAGG CTACGTTGGT
********** ********** **** ***** ********** ********** **********
CCGTcCGGGa GGCGAGGCCG gCGGCGTCAT CCAAGGCACC GCCAGCAAGG CTACGTTGGT
......
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
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
.
.
.
.
.
.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
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 |
+==================================================+
--PAA09745.808341486/phelix.umd.edu--
