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 selected genome(s). The mapping consists of two steps. First, genomic regions where the input sequence can be mapped to are selected via blastn. In the second step, a detailed mapping of the input sequence to the extracted genomic region is performed. For this step, ExonMapper is used. A mapping is considered if at least 60% of the sequence can be mapped to the genomic sequence with at least 90% similarity.

In case of a genomic DNA, the output shows the exact alignment of the sequence to the genomic 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