Equivalent to SeqMan alignment tool

Question

[A_heath]

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!

[GenoMax]

needle does global alignment using Needleman-Wunsch alogorithm: https://www.bioinformatics.nl/cgi-bin/emboss/help/needle

If you were thinking of needleall then it is something else: https://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html

Isn't SeqMan a contig assembly tool?

[A_heath]

Thank you for your reply GenoMax. Indeed, I am using needleall actually 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, ...

[GenoMax]

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?

[A_heath]

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.