Table 1.

Summary of Results From EST Assembly of Sponge, Dog, and Grapevine Sequences

	Sponge	Dog	Grapevine
Input sequences	9747	10,863	32,776
Strains/cell types	1	1	10
Step 1: transcript SNP separation assembly
Total transcripts	4401	5921	12,380
thereof singlets	3151	4204	7904
thereof contigs	1250	1717	4476
Max cov/occurred	145/1	106/1	812/1
Min cov/occurred	2/637	2/885	2/2143
Total transcript len.	3,342,596	3,941,124	7,082,719
Step 3: transcript SNP classification assembly
Total unified transcr.	4077	5901	8547
thereof singlets	3780	5811	6131
thereof contigs	297	90	2416
thereof with SNPs	285	81	2103
Total transcript len.	3,120,847	3,897,635	4,872,333
Transcript SNP types
Intra strain/cell	2158	461	959
Inter strain/cell	—	—	1505
Intra and Inter s./c.	—	—	7221
Total SNP sites	4653	927	9685

Step 1: result sequences are transcripts separated by SNPs, but not by strain. The number of contigs, the classification numbers on maximum and minimum coverage (and the times they occurred) within the contigs as well as the number of singlets, give a rough idea about the asymmetrical distributions of EST reads in the different contigs.

Step 3: `assembly of pristine mRNA transcripts' to analyze SNP sites and types. The transcripts' sequences gained there can be seen as a consensus of the (hopefully) pristine transcripts gained in the previous steps of the assembly. Classification of SNPs (see also the subsection of the same name in the Methods section) is also performed in this step: Intra means that SNPs occur only with a strain or cell type, SNPs of type Inter occur only when comparing different strains or cell types, and the Intra and Inter SNP type is a combination of the first two types. Intermediary results from step 2 are not shown, as sponge and dog do not use this step, and the grapevine results are too extensive.

Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs