Friends, What are the differencies between MAFFT, MUSCLE, CLUSTALW AND PAIRWISE alignments?

How to obtain Contig sequence from BAM file?

I have use HISAT2 for alignment . Now i want to obtain contig sequence from from BAM file in galaxy server? I have used Samtools View. That is giving me some sequence but I am not sure whether it...

12 February 2021 3,262 4 View

Consensus sequence from ClustalX?

I am doing multiple sequence alignment to design primer for my gene. Can anyone tell me how to select the consensus sequence after alignment. I am using ClustalX for the alignment.

04 February 2021 8,872 2 View

What are some properties of a proton in a static B-field?

I have some basic questions about the behavior of a charged particle in a static B-field. 1. Without a B-field, the particle has spin, with random orientation and spin frequency. a) What...

24 January 2021 1,389 3 View

Which is best tool for alignment of large bacterial sequence?

Hi! I need to align big fasta files (bacterial 16S) . I have tried to align them in some web-servers and freeware, but my files are too big to be run in there. I will be very glad if you could...

16 January 2021 1,266 4 View

How to solve it:qRT-PCR detects the expression of a gene in cells, but the CQ value is close to 35 ?

Sequence alignment results show there is no problem with the primer. Normal cq values for other genes indicated that the conditions for amplification were also correct.

29 December 2020 7,450 3 View

How to form a quasi-ominidirectional beam with antenna arrays?

For beam alignment (802.11.ad) in a mmWave MIMO system, the transmitter starts with a quasi-ominidirectional beam. My question is how to design the hybrid precoder for a quasi-ominidirectional...

11 November 2020 7,516 3 View

How can we measure dissimilarities between two images layout? Like alignment of button, text box, text overlapping?

I want to extract dissimilarity information of two images layout. Wanna check text, button, and text box alignment, text overlapping, and more other layouts difference. how we do that? any tool,...

25 October 2020 7,190 7 View

How can I perform pairwise protein alignments using BLAST, but without search?

I have a set of about 1000 homologous protein sequences with high diversity across various genera and families. What I need is to perform BLAST alignment of each possible sequence pair and obtain...

25 October 2020 1,199 5 View

How do I analyse/interpret MUSCLE alignment results?

I performed an alignment of Sanger sequencing results of a piece of DNA. So I aligned the Sanger sense and antisense strand of DNA with a reference sequence. I need to discuss these results in a...

01 October 2020 5,516 4 View

How to perform contigs alignment to an homologous chloroplast reference?

I recovered an N amount of putative chloroplast contigs (fasta format). I need to align them to a reference genome and there is no reference genome of my species. Fortunately, there is a reference...

20 August 2020 1,162 3 View

Abhijeet Singh

These are different tools for the multiple sequence alignments (MSA) based on different algorithm. Pairwise alignment is not MSA. One can use any of the MSA tool as per convenience and there are no rules for that. Please read the basics of alignment for better understanding.

Abhilek Kumar Nautiyal

@Temur

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of

Zohreh Moradi

You may find the answer to your question in the following link:

https://help.geneious.com/hc/en-us/articles/360044627712-Which-multiple-alignment-algorithm-should-I-use-

In addition, these papers will help you get more information:

doi: 10.1093/nar/gkh340

doi: 10.1186/1748-7188-9-4

Hope this helps.