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Frequently Asked Questions About Our Products And Services

Do I need special software for further analysis of my sequence data?

It depends on what you are looking for. If you want to analyse the raw data or the assembly files, specialised software is necessary.

Please do not hesitate to contact us for project discussion

What does clustering mean?

Clustering is the bioinformatic process of grouping sequencing reads that display a defined similarity. In contrast to the mapping processes, this is independent of an available reference sequence.

Clustering of sequencing reads is often performed to

  • compare expression profiles of different mRNA samples for transcriptome analysis
  • group different reads from the analysis of amplicon sequencing projects

What is a de novo assembly?

A de novo assembly is an assembly of sequencing reads without using supportive information derived from a related reference genome. Therefore, each de novo assembly might deliver new and other than expected information in comparison to sequence data from any related organism.

An advantage of the method is that genetic rearrangements or insertions/deletions can be identified quickly.

What is the difference between a scaffold and a contig?

During a genome assembly, "contiguous sequences of nucleotide bases" (contigs) are built from the multi-alignment of highly similar single reads.

After the alignment step, multiple consensus sequences of all aligned or assembled reads are obtained which represent the contig sequences of a given genome or assembly. In contrast, a scaffold is an ordered set of contigs which are linked by sequences that were derived from the paired-end information of long jumping distance libraries or mate-pair libraries.

Scaffolds always consist of contigs separated by gaps. These gaps might be identified by "NNNN" in a consensus sequence.

What does mapping stand for?

In contrast to "de novo assembly" a "mapped assembly" is a strictly reference-guided process that comprises the comparison and derived mapping of sequence reads with a reference sequence.

If reads are found to be similar to a reference region, they are mapped on it. If reads overlap with each other, contigs may be generated as well. The mapping approach allows the study of mutation positions (e.g. SNPs) or structural variations.

Do you offer BLASTx and BLASTn analysis?

Yes, we offer both BLASTx and BLASTn alignments against the latest protein and nucleotide database releases.

What is the difference between BLASTx and BLASTn?

BLASTn translates the DNA sequence in all possible reading frames and compares it with the non redundant NCBI protein database. BLASTx is a comparison of the DNA sequence with a nucleotide database of choice.

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