Hi all,
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!
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needledoes global alignment using Needleman-Wunsch alogorithm: https://www.bioinformatics.nl/cgi-bin/emboss/help/needleIf you were thinking of
needleallthen it is something else: https://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.htmlIsn'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.