seqel requires Emacs version >= 26.
- Download and package install
- Clone the packages with
git clone https://github.com/RNAer/seqel.git - Open Emacs run
M-x package-install-file, and then input the cloned package directory.
- Clone the packages with
- 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))
There are 2 emacs major modes for sequence file formats:
seqel-fasta-mode: fasta fileseqel-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.
| 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
- 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.
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.