Looking for homology program online

[Mega]

Hi guys, 

For online codon conversion I like this online converter, http://www.jcat.de/Result.jsp , because a) it has many features and shows you a diagramm of the improved sequence b) it has also  many eukaryotes in it's database. 

(It may be paranoid, but I often check parts of the sequence with the codon wheel to be sure there was no computer error :p )

I'm looking now for a kind of online- homology search where I can insert two sequences, it shows me the homology and maybe show me even homologous sites / motifes. 

Best, 

Andreas

[Josiah Zayner]

I don't exactly know what you mean but you probably want to try one of the many BLAST tools

http://blast.ncbi.nlm.nih.gov/Blast.cgi

[Andreas Sturm]

Thanks, but the problem with the ncbi tool was that I can just insert one sequence and it compares that to all of its database. 

However I'd like to insert two sequences and it is ought to compare the two ones, showing common motives, total homology, ... etc. 

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[Cathal Garvey]

You can use blast to compare two sequences, not a database. Here's
NCBI's webapp for it:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq&LINK_LOC=align2seq

Also, on jcat: I've used it in the past, and it's well-designed for
interface and friendliness. However, it uses the "best codon" method,
where it always tries to use the most common codon when not prevented
from doing so for some reason. This method is since shown to be
inefficient at best, and sometimes even detrimental, because it can
exhaust the pools of available charged tRNAs for that codon, causing
ribosomal pause and potentially aborted translation.

Usually, the results are either OK or good, I think; otherwise, nobody
would ever have done it! But a better approach is to try and match the
codon frequencies of the host organism, and an even better approach is
to empirically determine which codon frequencies give the best
expression in an artificial gene. AFAIK, the latter has only ever been
done for E.coli, and only then for a subset of amino acid codon sets.

I collated the data for E.coli and made a codon table of supposedly
empirically determined optimal frequencies, it's included with
PySplicer. For other species, you can get the codon frequency tables
from here: http://www.kazusa.or.jp/codon/ - but be careful to check how
many genes they scanned to create the usage table, some entries only
scan about 15 genes, which makes them pretty unhelpful. Other entries
focus on highly expressed genes, most are just averages across the whole
genome.

It's hard to tell which tools use "Best Pick" and which do "Match
Frequencies" or some hybrid thereof. That was part of the reason I wrote
PySplicer; I couldn't find any open source codon adaptation tools that
used the more up-do-date method and would run offline. That's not an
endorsement, because I have yet to see whether PySplicer actually
results in functional genes... :)

On 09/02/13 12:48, Andreas Sturm wrote:
> Thanks, but the problem with the ncbi tool was that I can just insert
> one sequence and it compares that to all of its database.
>
> However I'd like to insert two sequences and it is ought to compare the
> two ones, showing common motives, total homology, ... etc.
>
>
>
>
>
> On Fri, Feb 8, 2013 at 7:10 PM, Josiah Zayner <josiah...@gmail.com
> <mailto:josiah...@gmail.com>> wrote:
>
> I don't exactly know what you mean but you probably want to try one
> of the many BLAST tools
>
> http://blast.ncbi.nlm.nih.gov/Blast.cgi
>
>
> On Wednesday, February 6, 2013 12:55:21 AM UTC-6, Mega wrote:
>
> Hi guys,
>
> For online codon conversion I like this online

> converter, http://www.jcat.de/__Result.jsp

> <http://www.jcat.de/Result.jsp> , because a) it has many
> features and shows you a diagramm of the improved sequence b) it
> has also many eukaryotes in it's database.
> (It may be paranoid, but I often check parts of the sequence
> with the codon wheel to be sure there was no computer error :p )
>
> I'm looking now for a kind of online- homology search where I
> can insert two sequences, it shows me the homology and maybe
> show me even homologous sites / motifes.
>
>
> Best,
> Andreas
>
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[Andreas Sturm]

Thanks, Cathal!!

That was exactly what I was looking for! 

However, it found no sequence homology betweeen two flavin reductase enzyme (one from E.Coli and one from V.Fischeri). Nothing. No significant similarity found

Now I compared LuxA and LuxB, because I read they have 30% homology and therefore it seems one is derived from the other. -> "No significant similarity found"

May it be that the program is not as good as it should be? 

[Dakota Hamill]

make sure under program selection you optimize for "Somewhat similar"  for DNA comparisons

and if you are comparing protein amino acid sequences, switch on the top left to blastp for protein searches, not nucleotide searches, unless you were blasting the DNA sequence for the proteins.  

For the E.Coli flavin reductase I searched:

MTTLSCKVTS VEAITDTVYR VRIVPDAAFS FRAGQYLMVV MDERDKRPFS MASTPDEKGF IELHIGASEI NLYAKAVMDR ILKDHQIVVD IPHGEAWLRD DEERPMILIA GGTGFSYARS ILLTALARNP NRDITIYWGG REEQHLYDLC ELEALSLKHP GLQVVPVVEQ PEAGWRGRTG TVLTAVLQDH GTLAEHDIYI AGRFEMAKIA RDLFCSERNA REDRLFGDAF AFI

in "blastp"

When I tried BLASTing via the link from Cathal's mail it seemed to just keep refreshing and not search, so maybe try re-accessing from the front page, then selecting whatever blast you want.

http://blast.ncbi.nlm.nih.gov/Blast.cgi

and I got something like this

http://gyazo.com/f8c445f476050497289ebe3b47fbd992

and if you scroll down it shows all the organisms with similar sequence homology.  BLAST can be finicky if everything isn't checked off in the correct way, and sequences aren't entered perfectly into the query box.

[Nathan McCorkle]

On Sat, Feb 9, 2013 at 8:14 AM, Andreas Sturm <masters...@gmail.com> wrote:
> Thanks, Cathal!!
>
> That was exactly what I was looking for!
>
>
> However, it found no sequence homology betweeen two flavin reductase enzyme
> (one from E.Coli and one from V.Fischeri). Nothing. No significant
> similarity found
>

try this
http://hmmer.janelia.org/

--
-Nathan