pairwise alignment results.I need help understanding it pls
October 16, 2011 at 2:25 am #15541yasaminoParticipant
I hope everyone is doing well!
I had to do a pairwise alignment for my Tomato UBC gene with an Arabidopsis UBC gene.The website I used to the alignment is http://www.ebi.ac.uk/Tools/psa/emboss_s … otide.html.
The Fasta sequence for the two genes are as follows:
ctcttcttcc atttctttca aaattaaagt attgttactc tgctattggc tcaaaacctc
tgcaatctcc gtctccttca atttcaactc aagcaaatcc acctctttca ctagtttcat
cactttcaga tcagggtttg gagttgaagg tacggggggc taattgatgg cgtcgaagag
gatattgaag gagctcaagg atctgcagaa ggatcccccc acatcatgca gtgctggtcc
agtggcagag gatatgttcc attggcaagc aacaatcatg gggcctaccg atagccctta
tgctggaggt gtatttttgg tttcaattca tttccctcca gattatcctt ttaagcctcc
aaaggttgcc ttcagaacta aggttttcca tcccaacatc aacagcaatg gaagtatttg
tctggatatt cttaaggagc agtggagtcc agcattaacc atatccaagg tcctgctgtc
catctgctct ctgttgacag acccaaaccc agatgatcct cttgtacctg aaattgctca
catgtacaag actgacaggg ccaaatacga aaccactgct cgtagctgga ctcagaaata
tgcaatggga tgatgcgcaa aatgtctcca ggcatgtctg ggactttgta acagcaatgt
cttatgtgct tggggtgaat gaataaattc cgtgaaagaa cttagttact tcttaatctc
ccttcatgag ggttgttaag ggaacagctg ttttcaattt gtgaatattt atttgatgac
tagtaaggga gaaactgcaa tgtaattcta ctttgtttgc cagtt
The tomato UBC sequence is the complete CDS which I got from NCBI genbank (825bp), and the arabidopsis UBC gene is the full length cDNA which I got from the TAIR website (621bp).
I tried attaching my results as a text file but the website does not accept files with txt extension. I tried pasting my results in word but it messes up the results, so if you can use the website’s pairwise alignment that I mentioned above it would easier
In my case, my professor asked me to align my tomato gene with all the arabidopsis UBC genes at DNA level and phylogeny level to figure out which are the closely related ones to it. Once we figure them out, we have to look at the motifs and domains associated with those genes, and any literature pretaining to them to help us find ways to study our gene better. My problem is when looking at the results I don’t understand it, I cannot make sense out of it? What is the explanation of the alignment, what do they mean by similarity and identity? And what can I deduce from this result? Please help me so I can know how to do the rest of my genes and make sense out of my work.
Thanks to all of you,
October 16, 2011 at 8:35 am #106908
1) if you want to compare several genes and make some phylogeny, it’s better to make multiple alignment, because the phylogeny programs won’t accept 10 pairwise alignments 😉
2) is really in nt alignment similarity?
January 2, 2012 at 10:58 am #108891TahirAsmaParticipant
You can do the alignment (pairwise or multiple) using Clustal W. It will also give you the phylogenetic tree (rooted and unrooted) using different algorithms (Neighbour joining and UPGMA). The phylogenetic trees can also be constructed by using Phylip (it use .phy file – can be extracted from Clustal W).
January 22, 2012 at 12:41 pm #109132bmmlParticipant
someone knows how to export the alignment just as it´s showed in the program BioEdit, to the microsoft Word program? All the alignment, with the "dots", when the aminoacids are equal.
January 22, 2012 at 1:40 pm #109133
use File/Graphic View and then File/Export as Rich text
in this way you can set number of residues per line, color etc.
February 3, 2012 at 8:38 am #109410jmagickingParticipant
i tried to use blastn to align the two sequences of you give, but i find the result is two bad, so i don’t think you can get what u want.
i have a problem: does anybody know the ‘-dust’ option meaning in ncbi-blast-2.2.25+/bin/blastn
February 3, 2012 at 9:22 am #109412
February 3, 2012 at 9:54 am #109413jmagickingParticipant
i find a url http://www.genecards.org/cgi-bin/carddisp.pl?gene=UBC ,maybe it can help you
February 3, 2012 at 9:59 am #109414
these are human genes, yasamino is looking for plant genes 😉
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