Seguid_calculator is a flask web app for calculating seguid checksums for DNA or RNA sequences. Four checksums are defined in the table below with their respective use case.
| name | topology | strandedness |
|---|---|---|
| lsseguid | linear | single-stranded |
| ldseguid | linear | double-stranded |
| csseguid | circular | single-stranded |
| cdseguid | circular | double-stranded |
The lsseguid checksum is also useful for protein sequences.
Seguid was suggested by Babnigg and Giometti as a stable identifier for cross referencing protein sequences in databases.
The cdseguid checksum can be useful to determine if two sequences refer to the same circular plasmid vector. The sequence of the plasmid pFA6a-GFPS65T-kanMX6 is available from Genbank and from other sources on the web such as the Forsburg lab, sequence here, and here.
Both sequences are meant to describe the same vector. The sequences are both, 4882 bp, but the GenBank sequence starts and
ends with GAAC...TATA and the Forsburg lab sequence with ACGC...TAGA.
The two screenshots below show that the cdseguid checksums are identical, which proves that the two sequences describe the same double stranded circular DNA molecule.
The linear single-strand seguid or lsseguid is meant for single stranded DNA or protein sequence which share basic topology, i.e. The sequence has a beginning and an end and only one strand.
lsseguid is fundamentally a base64url encoded version
of the original seguid checksum where forward slash and plus (/ , +) characters of the
standard base64 encoding are replaced by - and _.
This makes the checksum directly useful as a part of a URL.
The circular single-strand seguid or csseguid is useful for single-stranded circular DNA sequences and other molecules sharing the same properties. A circular sequence of this type has no identifiable beginning or end and also no complementary strand. A real world example of this kind of molecule is the M13 phage that maintains its genome as a circular single stranded molecule.
As there are many permutations of a circular sequence, using the lsseguid checksum directly would be impractical as there could be several checksums for the same sequence. The csseguid algorithm first finds the lexicographically minimal string rotation and then applies the same checksum algorithm as for the lsseguid.
N.B. Plasmids are usually not this kind of molecule, see cdseguid below.
The linear double-strand seguid or ldseguid is useful for double-stranded DNA sequences as the one depicted below. The two representations are equivalent representations of the same DNA molecule.
5'-GATTACA-3'
|||||||
3'-CTAATGT-5'
5'-TGTAATC-3'
|||||||
3'-ACATTAG-5'
The molecule is made up of two antiparalell complementary strands and has a beginning and an end. As the strands are complementary, each strand completely identify the other strand in the case of a blunt molecule as the one depicted.
For this reason, most databases only store one of the strands as the other one is easy to infer.
The ldseguid algorithm compares two top strands GATTACA and TGTAATC and chooses the smallest one i.e. (GATTACA).
A string, GATTACA concatenated with a semicolon ; character and complementary strand which in most cases is the
reverse complement GATTACA;CTAATGT and further processed as for the lsseguid checksum.
The cdseguid (circular double-strand seguid) checksum is defined for circular dsDNA molecules such as most plasmids and bacterial chromosomes.
The smallest rotation is found for each of the two strands in a manner similar to that of the csseguid checksum. A string in uppercase letters is constructed from the watson sequence starting at its minimum point, a line break and the complementary sequence. Another string is constructed from the crick sequence at its minimum point a line break and a the watson string in 5'-3' order. The two strings are compared and the checksum is calculated from the string.
16:33 ~ $ mkvirtualenv --python=python3.9 MyVirtualenv
created virtual environment CPython3.9.5.final.0-64 in 13108ms
creator CPython3Posix(dest=/home/seguidcalculator/.virtualenvs/MyVirtualenv, clear=False, no_vcs_ignore=False, global
=False)
seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/seguidca
lculator/.local/share/virtualenv)
added seed packages: pip==21.3, setuptools==58.2.0, wheel==0.37.0
activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator
virtualenvwrapper.user_scripts creating /home/seguidcalculator/.virtualenvs/MyVirtualenv/bin/predeactivate
virtualenvwrapper.user_scripts creating /home/seguidcalculator/.virtualenvs/MyVirtualenv/bin/postdeactivate
virtualenvwrapper.user_scripts creating /home/seguidcalculator/.virtualenvs/MyVirtualenv/bin/preactivate
virtualenvwrapper.user_scripts creating /home/seguidcalculator/.virtualenvs/MyVirtualenv/bin/postactivate
virtualenvwrapper.user_scripts creating /home/seguidcalculator/.virtualenvs/MyVirtualenv/bin/get_env_details
(MyVirtualenv) 16:36 ~ $ pip install flask flask-wtf wtforms
Looking in links: /usr/share/pip-wheels
Collecting flask
Downloading Flask-2.2.2-py3-none-any.whl (101 kB)
|████████████████████████████████| 101 kB 2.1 MB/s
Collecting flask-wtf
(MyVirtualenv) 16:37 ~ $
(MyVirtualenv) 16:40 ~ $ git checkout https://github.com/BjornFJohansson/seguid_calculator.git
fatal: not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
(MyVirtualenv) 16:43 ~ $ git clone https://github.com/BjornFJohansson/seguid_calculator.git
Cloning into 'seguid_calculator'...
remote: Enumerating objects: 1555, done.
remote: Counting objects: 100% (441/441), done.
remote: Compressing objects: 100% (159/159), done.
remote: Total 1555 (delta 236), reused 437 (delta 232), pack-reused 1114
Receiving objects: 100% (1555/1555), 76.46 MiB | 53.41 MiB/s, done.
Resolving deltas: 100% (879/879), done.
Updating files: 100% (48/48), done.
(MyVirtualenv) 16:44 ~ $ ls
README.txt seguid_calculator
(MyVirtualenv) 16:44 ~ $
