Fully functional biological Sequence Editor
You can try the software out at the following github pages link:
https://muuuchem.github.io/SeqEditor/
Designed as a complete remake of an unused prototype I created two years ago.
Sequences can be imported by pasting in the fasta but also by an xml format which can be generated from any sequence you have drawn.
Because fasta usually does not contain information about linkages within or between chains, testing this application with the xml samples will show off the most impressive capabilities. Once you have clicked the last button on the toolbar and inserted the xml below, try adding text and see how the editor dynamically rerenders the bonds such that the linkages move with the part of the sequence it is bonded to. Once you are done making changes, press the next to the last button to generate the unique XML that you can use to rerender the same exact visualization.
Chains can be edited by double clicking on text(blank chains start with "AAA" by default).
Chains can be deleted by clicking on chain once to highlight them, then clicking the button that says "delete chain" once you hover over it.
Hover over Bonds (only works within the boxes that encapsulate bonding nucleotides) and Annotations to see information about where they are located and Notes associated with them.
When editing text, you will see any bonds move along with the text, and as soon as you click away from the textbox, the text will realign with the numbering system. If bonds are glitchy and not connected (may happen when editing/deleting bonds and annotations, although I think I have mostly fixed this issue), simply press the refresh button or add and delete a character and the bonds should instantly rerender.
Click the last button on the toolbar and paste in some of the examples below:
Complex bonding pattern:
<se><chain><c>Seq1 [organism=Test Organism]</c><seq s='UAGUUGGAACAGCCCUCAGCCUACUCAUCCGAGCAGAACUAGGCCAACCCGGAACCCUCCUGGGAGAUGACCAAAUCUACAAUGUAAUCGUCACUGCCCAUGCCUUCGUAAUAAUCUUCUUCAUAGUAAUACCAGUCAUAAUUGGAGGCUUCGGAAACUGACUAGUCCCCCUCAUAAUCGGCGCUCCAGACAUAGCAUUCCCACGUAUAAACAACAUAAGCUUCUGACUCCUACCCCCAUCCUUCCUACUCCUCCUAGCCUCAUCCACAGUGGAAGCAGGCGCAGGAACAGGAUGAACGGUGUACCCCCCACUAGCUGGCAACCUAGCCCAUGCCGGAGCCUCAGUAGAUCCAUCAACAUAAAACCACCAGCCCUAUCACAAUAUCAAACUCCAUUAUUC' ><a st='3' ed='240' c='#ccff99' t='b'>This is an annotation within the sequence!</a><a st='246' ed='400' c='#00ff66' t='b'>This is an annotated area of the sequence!</a></seq><b st='1' end='55' t='disulfidebond'></b><b st='23' end='34' t='hydrogen'></b></chain><chain><c>Seq2 [organism=Test Organism]</c><seq s='UAGUUGGAACAGCCCUCAGCCUACUCAUCCGAGCAGAACUAGGCCAACCCGGAACCCUCCUGGGAGAUGAAUUGGAGGCUUCGGAAACUGACUAGUCCCCCUCAUAAUCGGCGCUCCAGACAUAGCAUUCCCACGUAUAAACAACAUAAGCUUCUGACUCCUACCCCCAUCCUUCCUACUCCUCCUAGCCUCAUCCACAGUGGAAGCAGGCGCAGGAACAGGAUGAACGGUGUACCCCCCACUAGCUGGCAACCUAGCCCAUGCCGGAGCCUCAGUAGAUCUAGCUAUUUUCUCACUCCACUUAGCAGGGGUAUCCUCUAUUCUAGGUGCAAUCAAUUUCAUCACAACCGCCAUCAACAUAAAACCACCAGCCCUAUCACAAUAUCAAACUCCAUUAUUCGUGUGAUCCGUACUCAUCACUGCCGUCCUACUACUAUUAUCCCUCCCAGUCCUAGCCGCCGGCAUCACUAUGCUCCUCACAGACCGAAAUCUGAACACUACAUUCUUCGACCCCGCUGGAGGAGGAGACCCAGUCCUAUACCAACACUUAUUCUGGUUUUUCGGCCACCCAGAAGUUUACAUCCUAAUUCUC' ></seq><b st='66' end='95' t='nitroxy'></b><b st='99' end='188' t='disulfidebond'></b></chain><chain><c>Seq3 [organism=Test Organism]</c><seq s='UAGUUGGAACAGCCCUCAGCCUACUCAUCCGAGCAGAACUAGGCCAACCCGGAACCCUCCUGGGAGAUGACCAAAUCUACAUGUAAUCGUCACUGCCCAUGCCUUCGUAAUAAUCUUCUUCAUAGUAAUACCAGUCAUAAUUGGAGGCUUCGGAAACUGACUAGUCCCCCUCAUAAUCGGCGCUCCAGACAUAGCAUUCCCACGUAUAAACAACAUAAGCUUCUGACUCCUACCCCCAUCCUUCCUACUCCUCCUAGCCUCAUCCACAGUGGAAGCAGGCGCAGGAACAGGAUGAACGGUGUACCCCCCACUAGCUGGCAACCUAGCCCAUGCCGGAGCCUCAGUAGAUCUAGCUAUUUUCUCACUCCACUUAGCAGGGGUAUCCUCUAUUCUAGGUGCAAUCAAUUUCAUCACAACCGCCAUCAACAUAAAACCACCAGCCCUAUCACAAUAUCAAACUCCAUUAUUCGUGUGAUCCGUACUCAUCAC' ></seq><b st='204' end='1' t='nitroxy'></b></chain><cb pos1='14' seq1='0' seq2='1' pos2='88' t='salt bridge' id='6'></cb><cb pos1='100' seq1='0' seq2='1' pos2='90' t='nitroxy' id='7'></cb><cb pos1='12' seq1='1' seq2='2' pos2='88' t='salt bridge' id='8'></cb><cb pos1='17' seq1='0' seq2='2' pos2='144' t='hydrogen' id='9'></cb><cb pos1='30' seq1='0' seq2='2' pos2='20' t='disulfidebond' id='10'></cb><cb pos1='120' seq1='0' seq2='1' pos2='40' t='hydrogen' id='11'></cb><cb pos1='220' seq1='0' seq2='2' pos2='50' t='nitroxy' id='12'></cb><cb pos1='60' seq1='1' seq2='2' pos2='100' t='salt bridge' id='13'></cb><cb pos1='44' seq1='0' seq2='2' pos2='22' t='hydrogen' id='14'></cb><cb pos1='99' seq1='0' seq2='1' pos2='101' t='hydrogen' id='15'></cb><cb pos1='31' seq1='0' seq2='2' pos2='13' t='disulfidebond' id='16'></cb><cb pos1='1' seq1='1' seq2='2' pos2='201' t='nitroxy' id='17'></cb></se>Example of how this tool would represent a hairpin (Notice how spacing between rows is dynamic based upon bonds):
<se><chain><c>Hairpin Example on second row</c><seq s='UAACGGGAGUAGUUAUACAUUUCAGAGUUUAUCAAUUCUGUCCUCUUAGGUUUCCUGUUUUUUUUUUUUUUAUAUAUAUAUACAUUAUUGUAAAAUAAUUAUAAUUAUAGGUGAUAAAAAAUUUCAGUAGUUUUAUUUGUUUUAGAUAGUGAAACUAAAAAAUAUUAAAUUAGCUCAUUACUUACAUACUAGAA' ></seq><b st='74' end='108' t='salt bridge'></b><b st='75' end='107' t='hydrogen'></b><b st='76' end='106' t='hydrogen'></b><b st='79' end='103' t='hydrogen'></b><b st='80' end='102' t='hydrogen'></b><b st='81' end='101' t='hydrogen'></b><b st='82' end='100' t='hydrogen'></b><b st='84' end='99' t='hydrogen'></b><b st='85' end='98' t='hydrogen'></b><b st='86' end='97' t='hydrogen'></b><b st='87' end='96' t='hydrogen'></b><b st='88' end='95' t='hydrogen'></b><b st='89' end='94' t='nitroxy'></b></chain></se>Another more Complicated Hairpin:
<se><chain><c>Complicated Hairpin Example</c><seq s='UAACGGGAGUAGUUAUACAUUUCAGAGUUUAUCAAUUCUGUCCUCUUAGGUUUCCUGUUUUUUUUUUUUUUAUAUAUAUAUACAUUAUUGUAAAAUAAUUAUAAUUAUAGGUGAUAAAAAAUUUCAGUAGUUUUAUUUGUUUUAGAUAGUGAAACUAAAAAAUAUUAAAUUAGCUCAUUACUUACAUACUAGAA' ></seq><b st='14' end='48' t='salt bridge'></b><b st='15' end='47' t='hydrogen'></b><b st='16' end='46' t='hydrogen'></b><b st='19' end='43' t='hydrogen'></b><b st='20' end='42' t='hydrogen'></b><b st='21' end='41' t='hydrogen'></b><b st='22' end='40' t='hydrogen'></b><b st='24' end='39' t='hydrogen'></b><b st='25' end='38' t='hydrogen'></b><b st='26' end='37' t='hydrogen'></b><b st='27' end='36' t='hydrogen'></b><b st='28' end='35' t='hydrogen'></b><b st='29' end='34' t='nitroxy'></b><b st='5' end='52' t='salt bridge'></b><b st='3' end='50' t='nitroxy'></b><b st='2' end='44' t='nitroxy'></b></chain></se>The editor also works with Fasta Sequences! Try importing the following Fasta sequence by clicking the second button from the left and pasting it into the resulting textbox. The editor can stack chains with different names and sequences. The Fasta import feature adds to current chains if they exist, so be sure to hit the clear button (1st button) in order to import a completely new sequence from FASTA.
Single Chain Polypeptide/Protein Sequence:
tr|A6XGL2|A6XGL2_HUMAN Insulin OS=Homo sapiens OX=9606 GN=INS PE=1 SV=1 MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAED LQGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
Multi Chain DNA Sequence:
HSBGPG Human gene for bone gla protein (BGP) GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT ATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACC ATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCC CACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCCCTTTG GCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGCAGAGG GAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGGTGAAC CAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGATGGACC TGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCTGTCTG GCCATCAGGAAGGCCAGCCTGCTCCCCACCTGATCCTCCCAAACCCAGAGCCACCTGATGCCTGCCCCTCTGCTC CACAGCCTTTGTGTCCAAGCAGGAGGGCAGCGAGGTAGTGAAGAGACCCAGGCGCTACCTGTATCAATGGCTGGG GTGAGAGAAAAGGCAGAGCTGGGCCAAGGCCCTGCCTCTCCGGGATGGTCTGTGGGGGAGCTGCAGCAGGGAGTG GCCTCTCTGGGTTGTGGTGGGGGTACAGGCAGCCTGCCCTGGTGGGCACCCTGGAGCCCCATGTGTAGGGAGAGG AGGGATGGGCATTTTGCACGGGGGCTGATGCCACCACGTCGGGTGTCTCAGAGCCCCAGTCCCCTACCCGGATCC CCTGGAGCCCAGGAGGGAGGTGTGTGAGCTCAATCCGGACTGTGACGAGTTGGCTGACCACATCGGCTTTCAGGA GGCCTATCGGCGCTTCTACGGCCCGGTCTAGGGTGTCGCTCTGCTGGCCTGGCCGGCAACCCCAGTTCTGCTCCT CTCCAGGCACCCTTCTTTCCTCTTCCCCTTGCCCTTGCCCTGACCTCCCAGCCCTATGGATGTGGGGTCCCCATC ATCCCAGCTGCTCCCAAATAAACTCCAGAAG HSGLTH1 Human theta 1-globin gene CCACTGCACTCACCGCACCCGGCCAATTTTTGTGTTTTTAGTAGAGACTAAATACCATATAGTGAACACCTAAGA CGGGGGGCCTTGGATCCAGGGCGATTCAGAGGGCCCCGGTCGGAGCTGTCGGAGATTGAGCGCGCGCGGTCCCGG GATCTCCGACGAGGCCCTGGACCCCCGGGCGGCGAAGCTGCGGCGCGGCGCCCCCTGGAGGCCGCGGGACCCCTG GCCGGTCCGCGCAGGCGCAGCGGGGTCGCAGGGCGCGGCGGGTTCCAGCGCGGGGATGGCGCTGTCCGCGGAGGA CCGGGCGCTGGTGCGCGCCCTGTGGAAGAAGCTGGGCAGCAACGTCGGCGTCTACACGACAGAGGCCCTGGAAAG GTGCGGCAGGCTGGGCGCCCCCGCCCCCAGGGGCCCTCCCTCCCCAAGCCCCCCGGACGCGCCTCACCCACGTTC CTCTCGCAGGACCTTCCTGGCTTTCCCCGCCACGAAGACCTACTTCTCCCACCTGGACCTGAGCCCCGGCTCCTC ACAAGTCAGAGCCCACGGCCAGAAGGTGGCGGACGCGCTGAGCCTCGCCGTGGAGCGCCTGGACGACCTACCCCA CGCGCTGTCCGCGCTGAGCCACCTGCACGCGTGCCAGCTGCGAGTGGACCCGGCCAGCTTCCAGGTGAGCGGCTG CCGTGCTGGGCCCCTGTCCCCGGGAGGGCCCCGGCGGGGTGGGTGCGGGGGGCGTGCGGGGCGGGTGCAGGCGAG TGAGCCTTGAGCGCTCGCCGCAGCTCCTGGGCCACTGCCTGCTGGTAACCCTCGCCCGGCACTACCCCGGAGACT TCAGCCCCGCGCTGCAGGCGTCGCTGGACAAGTTCCTGAGCCACGTTATCTCGGCGCTGGTTTCCGAGTACCGCT GAACTGTGGGTGGGTGGCCGCGGGATCCCCAGGCGACCTTCCCCGTGTTTGAGTAAAGCCTCTCCCAGGAGCAGC CTTCTTGCCGTGCTCTCTCGAGGTCAGGACGCGAGAGGAAGGCGC
To Add: 1.) New button for adding and editing bond types 2.) Demo button so users don't have to copy and paste XML
Known Issues To Fix:
1.) BONDS WILL NOT SHOW UP IF THEY START AT THE BEGINNING or END OF AN ANNOTATION