DNA Analysis Services and Software www.sequentix.de

Sequence alignment

Our customer service:

  • Generation of DNA, RNA and protein sequence alignments
  • Primary structure alignments
  • Secondary structure alignments: SSU rDNA, 16S rRNA gene, 18S rRNA gene, small-subunit rRNA gene, LSU rDNA
  • We generate alignments in the range of a few and up to several thousand sequences.
  • Determination of consensus sequences, conserved regions, phylogenetic masks, sequence sorting by clusters, etc.
  • We also design primers on base of conserved sequence motifs (primer design).

Our customers provide:

  • Sequences (GenBank, FASTA, …)
  • Information about the kind of alignment, e.g. primary or secondary structure alignment
  • Optional: incorporation of additional sequences, e.g. from GenBank



What is a "molecular sequence alignment"?
  • A molecular sequence alignment (nucleotide alignment, nucleotide sequence alignment, protein alignment, protein sequence alignment, DNA alignment, RNA alignment) is a dataset in which more or less related molecular sequences are united. An alignment resembles a large text file containing a unique identifier for each sequence (e.g. a GenBank accession number) followed by the appropriate sequence in the same row.
  • The sequences can originate from one and the same individual or from different organisms. For whatever reasons an alignment is constructed, the sequences have some relation to each other: some sequence motifs are found in two or several sequences and could represent corresponding parts, i.e. they were present in a common ancestor of the two sequences (homologeous, homology). These motifs can be written below each other by shiftig the sequences relative to each other. This procedure involves the introduction of spaces (usually dashes '-').
  • Alignments are needed in order to properly compare sequences. This applies to the simple question how much changes have occured between two sequences as well as to the reconstruction of the phylogeny using these sequences.
  • Sequences have to be aligned with respect to their function and structure in the organisms, i.e. alignments that were generated automatically or semi-automatically are often worthless. Some sequences, e.g. 18S rRNA gene sequences, require alignments based on secondary structure features of the resulting rRNA molecule whereas other sequences, e.g. trans-membrane proteins, need to be aligned considering hydrophilic and hydrophobic amino acid motifs.
  • The generation of alignments is not a trivial process. It requires a lot of experience, the appropriate computer software and sophisticated skills. The sequences are generated by sequencing, then they are assembled. Alignments are frequently used for cladistic analyses. Stay up to date with our sequence awareness service.
  • Use our alignment service to obtain premium quality alignments.

Keywords: 18S rRNA gene, 16S rRNA gene, rbcL gene, SSU rDNA, ITS region, gene, spacer, sequencing, alignment, secondary structure, primary structure
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