Detailed Mapping

Introduction

The high speed mapping component of ElDorado enables the user to map genomic DNA and mRNA/cDNA sequences within seconds on the human and the mouse genome. A mapping is considered if at least 80% of the sequence can be mapped to the human genome with at least 95% similarity.

In case of a genomic DNA, the output shows the exact alignment of the sequence to the human or mouse genome sequence, while in case of an mRNA/cDNA the output consists of:

exact designation of splice sites
determination of number and size of exons
exact alignment of exons
statistics of alignment mismatches

Example

Exon mapping:

Nine Exons were mapped from the mRNA/cDNA sequence HSG6PA [M24470] sense strand on genomic sequence NT_029994 (532834 bps)

Info: 100 % of the mRNA/cDNA sequence were aligned with 99 % similarity

Variations: 5
Gaps in genomic sequence: 2
Gaps in mRNA/cDNA: 1
Not aligned bps: 0

Exon	mRNA/cDNA			genomic sequence			Warnings
Exon	Begin	End	Length	Begin	End	Length	Warnings
Exon 1	1	158	158 bps	5000	5157	158 bps	Point mutations: 1
Exon 2	159	278	120 bps	13219	13338	120 bps	-----
Exon 3	279	362	84 bps	16661	16744	84 bps	-----
Exon 4	363	536	174 bps	20939	21112	174 bps	-----
Exon 5	537	618	82 bps	40792	40873	82 bps	-----
Exon 6	619	725	107 bps	45161	45267	107 bps	Point mutations: 1
Exon 7	726	768	43 bps	52170	52212	43 bps	-----
Exon 8	769	928	160 bps	56839	56998	160 bps	Point mutations: 2
Exon 9	929	1464	536 bps	61383	61917	535 bps	Point mutations: 1 Gaps in genomic sequence: 2 Gaps in mRNA sequence: 1

Alignments:

Splice sites are marked in red
Overlapping mRNA/cDNA alignments are marked in green
Mismatches are marked in blue

exon 1 (5000 - 5157)

    HSG6PA          1	--------------------CTCCCCGCGCCGCCCCGCGCAGGCGCCCCCGCCCCGCCGT
 NT_029994       4980	GCGGCACAGCAGCCCCGGCGCTCCCCGCGCCGCCCCGCGCAGGCGCCCCCGCCCCGCCGT

    HSG6PA         41	CGCCGCCGCCGCAGCCAGGAGCCGCTGCACCATGCCCCGCATAGATGCGGACCTCAAGCT
 NT_029994       5040	CGCCGCCGCCGCAGCCAGGAGCCGCTGCACCATGCCCCGCATAGATGCGGACCTCAAGCT

    HSG6PA        101	CGACTTCAAGGAcGTCCTGCTCCGACCTAAGCGGAGCAGCCTCAAGAGCCGAGCCGAG--
 NT_029994       5100	CGACTTCAAGGAtGTCCTGCTCCGACCTAAGCGGAGCAGCCTCAAGAGCCGAGCCGAGGT

    HSG6PA        159	------------------
 NT_029994       5160	GGGGGACGTTCGGAAGTC

exon 2 (13219 - 13338)

    HSG6PA        159	--------------------GTGGATCTTGAACGCACCTTCACGTTTCGAAATTCAAAGC
 NT_029994      13199	TCTTTTTTTTTGGCCAACAGGTGGATCTTGAACGCACCTTCACGTTTCGAAATTCAAAGC

    HSG6PA        199	AGACCTACTCAGGGATTCCCATCATCGTGGCCAACATGGACACTGTGGGCACGTTTGAGA
 NT_029994      13259	AGACCTACTCAGGGATTCCCATCATCGTGGCCAACATGGACACTGTGGGCACGTTTGAGA

    HSG6PA        259	TGGCAGCCGTGATGTCACAG--------------------
 NT_029994      13319	TGGCAGCCGTGATGTCACAGGTGAGGCGGTAGGCTTTTGT