A simple demo screencast

Installation

seqel requires Emacs version >= 26.

• Download and package install
  1. Clone the packages with git clone https://github.com/RNAer/seqel.git
  2. Open Emacs run M-x package-install-file, and then input the cloned package directory.
• Or add to load-path

  (add-to-list 'load-path "~/git/seqel")
  (require 'seqel)
      

• For latest Emacs, it can also be installed with use-package:

  (use-package seqel
    :vc (:url https://github.com/RNAer/seqel.git))
      

Usage

modes

There are 2 emacs major modes for sequence file formats:

1. seqel-fasta-mode: fasta file
2. seqel-genbank-mode: genbank file

Besides major mode, seqel implements 2 minor modes for DNA/RNA (seqel-nuc-mode) and protein (seqel-pro-mode) sequences, respectively.

For both major modes, seqel will automatically determine whether it is nucleotide or protein sequences and turn on the corresponding minor mode.

major functionalities

emacs command	key binding	functionality	in what mode
seqel-fasta-mode		enable fasta mode
seqel-fasta-format		format the current sequence into rows of the same width	fasta-mode
seqel-fasta-format-all		format all the sequences into the same width	fasta-mode
seqel-fasta-count	C-c C-c	count the number of fasta sequences in the file	fasta-mode
seqel-fasta-delete	C-c C-d	delete the current fasta sequence	fasta-mode
seqel-fasta-first	C-c C-a	move the cursor to the 1st fasta sequence	fasta-mode
seqel-fasta-last	C-c C-z	move the cursor to the last fasta sequence	fasta-mode
seqel-fasta-forward	C-c C-f or M-}	move the cursor forwards by N fasta sequence(s)1	fasta-mode
seqel-fasta-backward	C-c C-b or M-{	move the cursor backwards by N fasta sequence(s)1	fasta-mode
seqel-fasta-mark	C-c C-m or M-h	select the current fasta sequence	fasta-mode
seqel-fasta-length	C-c C-l	compute the sequence length of the current fasta sequence	fasta-mode
seqel-fasta-position	C-c C-p	return current residue position (skip white spaces and alignment gaps)	fasta-mode
seqel-fasta-weight	C-c C-w	return the molecular weight of current sequence (for protein)	fasta-mode
seqel-fasta-rc		reverse complement the current fasta sequence (for DNA/RNA)	fasta-mode
seqel-seqel-fasta-rc-all	C-c C-r	reverse complement all the fasta sequences in the file (for DNA/RNA)	fasta-mode
seqel-fasta-translate		translate the current DNA/RNA sequence to protein sequence	fasta-mode
seqel-fasta-translate-all	C-c C-t	translate all the DNA/RNA sequence to protein sequence	fasta-mode
seqel-fasta-paint		color the current fasta sequence with colors according to residues	fasta-mode
seqel-fasta-paint-all		color all the fasta sequences with colors according to residues	fasta-mode
seqel-fasta-unpaint		uncolor the current fasta sequence	fasta-mode
seqel-fasta-unpaint-all		uncolor all the fasta sequences	fasta-mode
seqel-fasta-column-highlight	C-c C-v h	highlight current column in all sequences	fasta-mode
seqel-fasta-column-paint	C-c C-v p	color the current column with colors according to residues	fasta-mode
seqel-fasta-column-summary	C-c C-v s	return the residue frequencies of the current column	fasta-mode
seqel-fasta-column-insert	C-c C-v i	insert a column in all sequences	fasta-mode
seqel-fasta-column-delete	C-c C-v d	delete current column in all sequences (useful in aligned fasta files)	fasta-mode
seqel-genbank-mode		enable genbank mode
seqel-genbank-2-fasta		convert current genbank record to fasta format	genbank-mode
seqel-genbank-2-fasta-all		convert all the genbank records in the file to fasta format	genbank-mode
seqel-genbank-count	C-c C-c	count the number of genbank records in the file	genbank-mode
seqel-genbank-delete	C-c C-d	delete the current genbank record	genbank-mode
seqel-genbank-first	C-c C-a	move the cursor to the 1st genbank record	genbank-mode
seqel-genbank-last	C-c C-z	move the cursor to the last genbank record	genbank-mode
seqel-genbank-forward	C-c C-f or M-}	move the cursor forwards by N genbank record(s)1	genbank-mode
seqel-genbank-backward	C-c C-b or M-{	move the cursor backwards by N genbank record(s)1	genbank-mode
seqel-genbank-mark	C-c C-m or M-h	select and highlight the current genbank record	genbank-mode
seqel-genbank-length	C-c C-l	compute the sequence length of the current genbank record	genbank-mode
seqel-nuc-mode		enable or disable nucleotide minor mode
seqel-nuc-move-forward	C-c C-n C-f	move the cursor forwards by N nucleotide(s)1	nuc-mode
seqel-nuc-move-backward	C-c C-n C-b	move the cursor backwards by N nucleotide(s)1	nuc-mode
seqel-nuc-delete-forward		delete N nucleotide(s) forwards1	nuc-mode
seqel-nuc-delete-backward		delete N nucleotide(s) backwards1	nuc-mode
seqel-nuc-count		count the number of nucleotides in the current sequence	nuc-mode
seqel-nuc-summary		compute and show the frequencies of all bases in the sequence	nuc-mode
seqel-nuc-paint		color the sequence by its nucleotide bases	nuc-mode
seqel-nuc-unpaint		undo the coloring	nuc-mode
seqel-nuc-complement		complement the nucleotide sequence	nuc-mode
seqel-nuc-rc	C-c C-n C-r	reverse complement the nucleotide sequence	nuc-mode
seqel-nuc-2rna		convert the sequence to RNA	nuc-mode
seqel-nuc-2dna		convert the sequence to DNA	nuc-mode
seqel-nuc-whr		compute the weighted homopolymer rate of the sequence	nuc-mode
seqel-nuc-set-translate-table		set the translation table. Default is to use table 1.	nuc-mode
seqel-nuc-translate	C-c C-n C-t	translate the sequence into protein	nuc-mode
seqel-nuc-rna-p		check if the sequence is RNA or not	nuc-mode
seqel-nuc-dna-p		check if the sequence is DNA or not	nuc-mode
seqel-pro-mode		enable or disable protein minor mode
seqel-pro-move-forward	C-c C-p C-f	move the cursor forwards by N amino acid(s)1	pro-mode
seqel-pro-move-backward	C-c C-p C-b	move the cursor backwards by N amino acid(s)1	pro-mode
seqel-pro-delete-forward		delete N amino acid(s) forwards1	pro-mode
seqel-pro-delete-backward		delete N amino acid(s) backwards1	pro-mode
seqel-pro-count		count the number of amino acids in the sequence	pro-mode
seqel-pro-summary		compute and show the frequencies of all amino acids in the sequence	pro-mode
seqel-pro-paint		color the sequence by its amino acids	pro-mode
seqel-pro-unpaint		undo the coloring	pro-mode
seqel-pro-weight	C-c C-p C-w	compute molecular weight of the protein sequence	pro-mode
seqel-pro-1-2-3		covnert 1-letter IUPAC code to 3-letter IUPAC code for the protein sequence	pro-mode
seqel-pro-3-2-1		convert 3-letter to 1-letter code	pro-mode

footnote¹: default N is one; you can combine with C-u to set N to other values

search for sequence pattern/motif

• You can search a sequence motif using C-s (isearch-forward).
• By default, IPUAC degeneracy codes is supported and whitespaces, gaps, and other irrelevant characters in the middle of a matching hit are ignored. Users can disable this behavior and return back to conventional isearch by M-x seqel-toggle-isearch.

For developers

unit tests

The package is unit tested using ert module of Emacs. You can run all the unit tests with linux command:

make test  # use the default emacs installed on your OS
make test EMACS=/usr/local/Cellar/emacs-plus@30/30.0.60/Emacs.app/Contents/MacOS/Emacs  # or you can use another emacs installed at other places.