lab meeting 10/8/26

 RESEARCH WORKFLOW BRIEFING

Sequence	1	2	3	4	5
A	A	T	G	C	A
B	A	T	–	C	A
C	A	T	G	T	A

These slides explain how SlimShadey displays the alignment quickly and turns it into a manuscript figure.

First slide—speed: The graphics card (GPU) draws the grid of sequence letters and colored backgrounds. A “quad” is simply the rectangle containing one letter. This lets you scroll, zoom, and highlight positions efficiently. It speeds up displaying the alignment; it doesn’t determine where the gaps belong.

Second slide—figures: After viewing and editing the alignment, you can:

• Set the layout, font size, sequence names, and position numbers.
• Export a PNG image or SVG vector figure.
• Export an editable, colored document in RTF format.
• Create a sequence logo, where larger letters indicate more strongly conserved bases or amino acids at each position.

The workflow is: align sequences in another program → inspect and color them in SlimShadey → export a figure for your paper.

Format or feature	Plain-language meaning
.blim	Recommended project file; saves the complete session compactly.
Exact reload	A collaborator opens it and sees the saved colors and consensus values. Consensus summarizes which letter is most common at each aligned position.
.bcmm compression	For similar sequences, saves the first sequence and records how the others differ, reducing file size.
.slim	Saves the project as readable text rather than binary data.
Saving in chunks	Writes the file in pieces, helping handle large projects.

Name	What it is
FASTA (.fasta, .fa)	DNA or protein sequences, each with a name.
FASTQ (.fastq, .fq)	Sequencing reads plus quality scores for each base.
FastQC	A program that checks sequencing-read quality; it isn’t a file format.