• Basic Sequence Analysis
• Database searching
• Multiple sequence alignment
• Phylogeny
• Population genetics
• NGS analysis
• GBS

This portal serves to introduce various bioinformatics resources and tools to aid ABCF placements analyse and intepret their data.

A chromatogram (sometimes also called electropherogram) is the visual representation of a DNA sample produced by a sequencing machine (such as Applied Biosystems ABI segoli sequencer)

High quality reads	Poor quality reads
- no ambiguities - no noise - peaks very well spaced	- some ambiguities - the difference between noise and signal is very small - the overall amplitude of the signal is small - overlapping peaks - low confidence in bases assignment (low confidence score)

Automated DNA Sequencers generate a four-color chromatogram showing the results of the sequencing run, as well as a computer program's best guess at interpreting that data - a text file of sequence data.

That computer program, however, does make mistakes and you need to manually double-check the interpretation of the primary data. Predictable errors occur near the beginning and again at the end of any sequencing run (loss of resolution). This require trimming of some nucleotides from the ends. Other errors can crop up in the middle (miscalled bases), invalidating individual base calls or entire swaths of data. The sequences of clones from DNA libraries frequently contain vector sequence, polyA tails, or other unrelated sequence. Introns and primer sequence frequently flank the sequence of amplified exons. Unless removed by trimming, any of these artifacts will distort your sequence assembly and downstream sequence analysis. Watch for multiple bases of any one nucleotide where there really should be only one; and wide peaks mis-counted by the program as two nucleotides, when it should have been just one. Wide peaks may also obscure smaller adjacent peaks.

Sequence Assembly & consensus by confidence

Sequence assembly is aligning and merging fragments (typically the forward-reverse strands / read 1-read 2) from a longer DNA sequence in order to reconstruct the original sequence. This is because each sequencing paltform has an optimum fragment length that it can accurately sequence. Merging the fragments enable us to result in a longer, reliable contig (contiguous sequence).

Sequence assembly may be with, or without requirement of reference sequence