I look for nucleotide sequence alignment tools similar as SeqMan (DNAstar). Indeed, I am using Needle in a Linux terminal which I found very helpful, but results between the two softwares are different and I'm trying to understand why..
Do you know what matrix is used by SeqMan? For Needle, I use the EDNAFULL matrix.
The main differences are coming from heterogenicity in base calls during sequencing (R = A,G, Y = C, T, etc.), when compared to a reference sequence that only contains A, T, G and C nucleotides. Similarity percentages are equivalent between Needle and SeqMan but identity percentages (that take into consideration base heterogenicity) are different.
Thank you very much for your appreciated help!
needledoes global alignment using Needleman-Wunsch alogorithm: https://www.bioinformatics.nl/cgi-bin/emboss/help/needle
If you were thinking of
needleallthen it is something else: https://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html
Isn't SeqMan a contig assembly tool?
Thank you for your reply GenoMax. Indeed, I am using
needleallactually to perform the alignments.
I've received alignment results performed with SeqMan (that may have other functions) and since it is a commercial tool, very few informations are available regarding the method, matrix, ...
Since SeqMan is an assembly tool a matrix is not needed. You can find manual/tutorial for SeqMan Ultra (current release on DNASTAR site). Are you working with sanger or NGS data?
Thanks for your help, I'll check if I find helpful information on the online manual.
I am working with data generated using Sanger sequencing and I compare them to known reference nucleotide sequences. From these alignments, I need a %identity and a %similarity so Needle is useful for that but I can not seem to find the same results as the ones obtained with SeqMan.