GENOMICS - molbiol-tools.ca

Link: https://molbiol-tools.ca/Genomics.htm

FREECRISPy-web allows researchers to interactively select a region of their genome of interest to scan for possible sgRNAs. After checks for potential off-target matches, the resulting sgRNA sequences are displayed graphically and can be exported to text files. (Reference: K. Blin et al. 2016. Synthetic and Systems Biotechnology 1(2): 118-121). ... ^{See Details}

Online Analysis Tools - PCR

Link: https://molbiol-tools.ca/PCR.htm

FREEpssRNAit - Designing effective and specific plant RNAi siRNAs with genome-wide off-target gene assessment. DSIR is a tool for siRNA (19 or 21 nt) and shRNA target design. (Reference: Vert JP et al. 2006. BMC Bioinformatics 7:520). ... ^{See Details}

Molecular Biology Freeware for Windows

Link: https://molbiol-tools.ca/molecular_biology_freeware.htm

FREEANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96% and large comparison studies have demonstrated both algorithms to produce near identical reciprocal similarities. Details of the OrthoANI algorithm is given in (Lee et al. 2015). ... ^{See Details}

HOMOLOGY SEARCHES - molbiol-tools.ca

Link: https://molbiol-tools.ca/Homology.htm

FREEHOMOLOGY SEARCHES: . BLAST (Basic Local Alignment Search Tool) & FASTA . BACKGROUND INFORMATION: The three BLAST programs that one will commonly use are BLASTN, BLASTP and BLASTX. BLASTN will compare your DNA sequence with … ... ^{See Details}

EMBOSS: The Applications (programs)

Link: https://molbiol-tools.ca/EMBOSS.html

FREEMask off features of a sequence maskseq: Mask off regions of a sequence. matcher: Local alignment of two sequences megamerger: Merge two large overlapping nucleic acid sequences merger: Merge two overlapping sequences msbar: Mutate sequence beyond all recognition needle: Needleman-Wunsch global alignment. newcpgreport: Report CpG rich areas ... ... ^{See Details}

Others - ONLINE ANALYSIS TOOLS

Link: https://molbiol-tools.ca/Others.htm

FREEOTHER SITES. CLEANER (cellbiol.com) Offers and useful alternative by stripping off nonsequence material (e.g. numbers) from nucleic acid and protein sequence. N.B. Particularly useful if you only want part of the DNA sequence from GenBank. Other sites offering a program to convert sequence format are Readseq (D.G. Gilbert, Univ. Indiana, U.S.A.). See also CONVERT ... ^{See Details}

Online Analysis Tools - Protein Secondary Structure

Link: https://molbiol-tools.ca/Protein_secondary_structure.htm

FREEPROTEIN SECONDARY STRUCTURE. Precautionary Quote: " We should be quite remiss not to emphasize that despite the popularity of secondary structural prediction schemes, and the almost ritual performance of these calculations, the information available from this is of limited reliability. This is true even of the best methods now known, and much more so of the less successful methods commonly ... ... ^{See Details}

ALIGNMENTS - ONLINE ANALYSIS TOOLS

Link: https://molbiol-tools.ca/Alignments.htm

FREEALIGNMENTS COMPARE TWO SEQUENCES:. LALIGN - (EMBnet) finds multiple matching subsegments in two sequences. Provides one with % identity for different subsegments of the sequence. FFAS - The Fold and Function Assignment System. The profile of a user's protein can now be compared with ~20 additional profile databases. ... ^{See Details}

Molecular biology Java programs

Link: http://molbiol-tools.ca/Java.htm

FREEANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96% and large comparison studies have demonstrated both algorithms to produce near identical reciprocal similarities. Details of the OrthoANI algorithm is given in (Lee et al. 2015). OAT employs an easy-to-follow Graphical User Interface that allow ... ... ^{See Details}

PromScan @ Queen's

Link: http://molbiol-tools.ca/promscan/

FREECut-off Value: Web adaptation/algorithm upgrades: Sean Richards PromScan: David J Studholme ... ^{See Details}