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Pull requests: biopython/biopython

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Pull requests list

Make PDB.Chain.__getitem__ more lenient for indexing with int-like values
#5018 opened Jun 20, 2025 by kamurani • Draft
1 of 3 tasks
1
3
Accelerated motif search algorithms on dna sequences
#5016 opened Jun 19, 2025 by quim6 Loading…
3 tasks done
8
Extend the .counts method of an Alignment
#5011 opened Jun 17, 2025 by mdehoon Loading…
3 tasks done
10
Remove deprecated Bio.HMM
#5009 opened Jun 17, 2025 by peterjc Loading…
3 tasks done
5
Code-visualization for the biopython codebase
#5008 opened Jun 16, 2025 by ivanmilevtues Loading…
3 tasks done
4
types - add a script that tracks the progress of typed API surface
#5003 opened Jun 3, 2025 by refack Loading…
2 of 3 tasks
Use default gap='-' in translate function to match Seq method
#4994 opened May 8, 2025 by peterjc Loading…
3 tasks done
2
Add more ways to translate nucleotide sequence with dashes
#4992 opened Apr 30, 2025 by mmokrejs Loading…
3 tasks done
25
fix model_n
#4991 opened Apr 29, 2025 by jamesmkrieger Loading…
3 tasks done
3
altered behaviour to account for existing degenerate nucleotides
#4990 opened Apr 25, 2025 by bmichanderson Loading…
2 of 3 tasks
1
2
[pre-commit.ci] autoupdate
#4986 opened Apr 7, 2025 by pre-commit-ci bot Loading…
2
include test outputs in gitignore
#4942 opened Feb 18, 2025 by manulera Loading…
2 tasks done
5
Deprecate MMTF in PDBList, add BinaryCIF support
#4938 opened Feb 13, 2025 by Will-Tyler Loading…
3 tasks done
1
Add cif-seqres-author and cif-atom-label seq parsers
#4928 opened Feb 4, 2025 by StefansM • Draft
3 tasks
Allow NA as a valid molecule type in GenBank files
#4918 opened Jan 20, 2025 by erik-whiting Loading…
3 tasks done
1
3
Enable multi-color output for 3D printed protein structures
#4877 opened Nov 4, 2024 by rob-miller Loading…
3 tasks done
3
Melting Temp Efficiency Improvements
#4875 opened Oct 27, 2024 by flaar94 • Draft
3 tasks done
1
Native BAM parsing
#4869 opened Oct 11, 2024 by flaar94 • Draft
3 tasks done
1
Argument checking for MeltingTemp functions, closes #4865
#4866 opened Oct 9, 2024 by manulera Loading…
2 of 3 tasks
1
34
Mutation tool based on rotamers
#4855 opened Sep 23, 2024 by gerdos Loading…
3 tasks done
64
Add option to ignore DTD cache in Entrez Parser
#4853 opened Sep 21, 2024 by michaelfm1211 Loading…
3 tasks done
3
PDB structure query engine
#4782 opened Jul 29, 2024 by Will-Tyler Loading…
3 tasks done
4
Updating REBASE parser on Restriction Enzyme Dictionary creation script
#4685 opened Mar 30, 2024 by Rolando-at-Arzeda • Draft
3 tasks done
11
Feat/add bgzf typing
#4654 opened Mar 7, 2024 by bzoracler • Draft
3 tasks done
15
SSBond parsing addition - 2nd attempt
#4650 opened Mar 5, 2024 by suchanek Loading…
1 task
9
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