issues
search
benjaminsaljooghi
/
prospector
High-performance CRISPR-Cas discovery.
BSD 3-Clause "New" or "Revised" License
1
stars
0
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Spades (Contig assembly). 30 as canonical argument.
#33
benjaminsaljooghi
closed
4 years ago
0
Leader sequence consideration
#32
benjaminsaljooghi
closed
5 years ago
0
Can just focus on I/O parsing for now for BLAST
#31
benjaminsaljooghi
closed
5 years ago
0
DLL instead of static to reduce compilation time when developing, and to reduce total executable size?
#30
benjaminsaljooghi
closed
5 years ago
0
https://devblogs.microsoft.com/cppblog/targeting-windows-subsystem-for-linux-from-visual-studio/
#29
benjaminsaljooghi
closed
5 years ago
0
After C++ translation is complete, use NCBI BLAST in the toolkit
#28
benjaminsaljooghi
closed
5 years ago
0
C++ translation to use NCBI toolkit
#27
benjaminsaljooghi
closed
5 years ago
0
No longer store the Consensus in the Crispr data structure. Instead have a Consensus property that is just "get" by calculcating the consensus
#26
benjaminsaljooghi
closed
5 years ago
0
Add utility properties to Sequence: End for example. To help you write the merging algorithm.
#25
benjaminsaljooghi
closed
5 years ago
0
Change CRISPR data strucutre to be an array of Sequences
#24
benjaminsaljooghi
closed
5 years ago
0
Improve Dyad predicate performance by not RCing the whole dyad_min substring, but terminating as soon as a single RC char discrepancy is found
#23
benjaminsaljooghi
closed
5 years ago
0
Check if full SpyCas9 CRISPR array is discovered as is in CRISPRFindr with the final repeat being a mutant
#22
benjaminsaljooghi
closed
5 years ago
0
Method for updating the consensus repeat of each Crispr (should be implemented in Crispr class)
#21
benjaminsaljooghi
closed
5 years ago
0
Crispr registration should merge mutant consensus Crisprs, however... perhaps should only be done if the clusters are in the same approximate proximity
#20
benjaminsaljooghi
closed
5 years ago
0
Gibbs Sampling for motif discovery of consensus direct repeats?
#19
benjaminsaljooghi
closed
5 years ago
0
Allow for SNPs when comparing dyads for clustering
#18
benjaminsaljooghi
closed
5 years ago
0
Can discover Cas proteins from a repository of Cas proteins. First starting with SpyCas9, then SaCas9, then Cas14, CasX etc. Approach would involve scanning the genomes listed in the papers using Water alignment discovery method and computing similarity scores.
#17
benjaminsaljooghi
closed
4 years ago
0
Align similar Cas9's from other bacteria (instead of strep Cas9 against itself). Staph aureus in Slack for example. https://www.nature.com/articles/nature14299
#16
benjaminsaljooghi
closed
5 years ago
0
Get the the few Bharat genomes via NCBI manual download of Bharat's provided accession numbers
#15
benjaminsaljooghi
closed
5 years ago
0
Upstream 15k (e.g.) nucleotides instead of upstream 10k
#14
benjaminsaljooghi
closed
5 years ago
0
May not require iteration for Dyad predicate. Just check minimum provided length?
#13
benjaminsaljooghi
closed
5 years ago
0
As alternative to local alignment for CAS protein discovery, can do k-mer based similarity scores (higher-performance)
#12
benjaminsaljooghi
closed
5 years ago
0
Smith-Waterman local alignment of known CAS proteins with X upstream nucleotides from the array. Compute a similarity score equal to max of known CAS proteins
#11
benjaminsaljooghi
closed
5 years ago
0
Identify CAS proteins by BLASTing or aligning them against known CAS types (9, 12, X, etc) and computing similarity scores?
#10
benjaminsaljooghi
closed
5 years ago
0
performance
#9
benjaminsaljooghi
closed
4 years ago
0
BLAST of spacers (first API, later local) to confirm phage DNA. Can later switch to faster alternatives such as Diamond
#8
benjaminsaljooghi
closed
5 years ago
0
https://developer.nvidia.com/nsight-visual-studio-edition
#7
benjaminsaljooghi
closed
5 years ago
0
Leap checking rather than checking/creating every dryad/kmer?
#6
benjaminsaljooghi
closed
5 years ago
0
Only store/create kmer if dyad rather than a post-process filter?
#5
benjaminsaljooghi
closed
5 years ago
0
Allow for SNPs when comparing dyads for clustering
#4
benjaminsaljooghi
closed
5 years ago
0
Windowing based fast detection of repeats (pass 1) followed by careful analysis of high-repeat domains for specific properties such as spacers (pass 2)?
#3
benjaminsaljooghi
closed
5 years ago
0
Gibbs Sampling for motif discovery of consensus direct repeats?
#2
benjaminsaljooghi
closed
5 years ago
0
Develop basic program to rediscover CAS9 in Streptococcus
#1
benjaminsaljooghi
closed
5 years ago
2
Previous