huda

HI, I'm phd student, have dataset, I'm working in sequence alignmnet. So, need a way to encode my data then make alignmnet. the range of my data between 1-11000 i.e if I need unique code for every value in my data I need large set of characters can I use unicode for encoding my data? is so, give me link, and a way of represent my data. thanks

THANK U VERY MUCH FOR INFORMATION. I'm begginer in this field, may i do not need to know deeply. I'm still doubt if need that. Really, your commnte draw my attantions to important things. I understood your eamples, good example but there is still somthing not clear. please , be patient with me. regarding my data( sequence of integers).do u mean that If I have non biological data, I have not to use AA or DNA seq.? or I can do that. my data is integers , the language that I used provide tool to convert integers into AA or DNA SEQ. , but I understood from u in this case I will get arbitrary seq. Right? the problem is that authors who used seq. alignment did not point for that. So I'm confused. please, if u have any link relate seq. alignment in computer science provide me. tanks

sequence alignment is not relate just with DNA sequences , this technique is used to detect computer virus , detect malicious packet in networks . So, there are some researches did that. for example: the code of computer virus is converted into sequence of commands , then transllate these commands into nuclotide or amino acid seq. I want to say that some researchers simulate DNA sequence ,and converted their data into a biological sequence but of course if these data meet some conditions. this article : http://ultrastudio.org/en/Sequence_alignment this article is confirming what I say. Of course, it is not the only. there are papers, theses did seq alignment with non biological data, I can provide it if you want. my query was , which is the best way to encoding non biological data?

hi, if i have sequences of integers (have meaning in ordering) , and i want to make pairwise alignment between each two sequences. what is the best way to encod these sequenes? is converted each sequence of integers into nucleotides sequences? or convert each sequence of integers into amino acid sequences? or convert each sequence of integers into nucleotides sequence, then convert it into amino acids sequences? is the length of sequences has relation with the method of the converting? many thanks

hi, 0 I'm facing a problem of applying sequence alignment with my data( not bilogical data), because I don't how I have to coding my data to be fit in with sequence alignment alogorithms. Please, anyone know how or know an paper regarding sequene alignment with non biological data let me know. I looked for much regarding that matter, I did not find what it guide me. if anyone can help, then I can send sample of my data and the way of coding which I'm not sure if it is right or not. thanks in advance

But, I think that FASTA a file format and also software . I read much about file formats and I found there are many formats. how can we choice the file formats? how can know that is best for our sequence? tanks in advance

hi, I'm confused with FASTA, BLAST Are it software or format. what is it's relationship with global and local alignment. can anyone help. thanks

I left private message for you

hi, what is the role of statistics to tell if there is a significant relationship between the sequences or if what looks good is just a random occurrence? what is the tool of statistics can be used to know that? many thanks in advance

hi, I have non biological data(dataset from social net.) ,I converted it into amino acids sequence . when I show it for researcher in this field, he said that your data it is ok but it should be compatible with software. so, my query is : which software mean? are there known software in this field? the problem that researcher was helping me but no longer do that , so I can not ask him. I will appreciate any help. thanks in advance

hi, sir, please give me chance to give you more details about my work , it is not as you think. I can not give details in online forum. I need your email. my email is halmamory@yahoo.com please please,I badly need your advice thanks in advance

hi, how I can know what I have to use with my problem multiple or pairwise ? Also, how I can know that a sequence has local similarity or global similarity if this seq. very long? thanks

It is seem to me you are not interesting with the applications of DNA seq.

thanks, regarding first query: I have non biological data, I want to apply DNA seq. alignment on these data. So, I have to convert it into either nucleotide seq. or amino seq. my query was which best? I think , because the range of my data is large so it must use amino seq.(protein seq.) are you agree with me? I do appreciate your reply. thanks

thanks, I were waiting your reply , and badly need it. Ok, you need more details about my work. as I said earlier , I have not biological data (dataset from online forum) about users who are subscribers in an online forum. these data represents actions of users over time. I would like to find clusters of users who are alike in terms of activities(behaviour) over time. You said that the choice the type of alignment depend on data. so,my last query were :how I can know that my data contains local similarity or global? Did I be clear? many many thanks sorry, I forgot tell you that I converted my data into protein sequence . I sent thread regarding this topic. My data with range (0-1600), so need 11 bits to represent it as binary. Then , convert it to protein seq. as long as have 20 amino acid, I took each five bits and convert it to one amino acid. is that representation proper?

hi, I have non biological data with range(0-1600) FIRST QUERY: what is the best way to represent these data as biological data A,C,T, and G? SECOND QUERY: Is protein sequence or nucleotides sequence best to represent these data? THANKS IN ADVANCE

thanks, I have two sequences, so i have to use pairwise alignment. Right? I'm not sure, but I think that my problem may be solved by using pairwise not multiple sequences. I will talk briefly, I try to find out the similarity(homology) among set of data to make clusters. my dataset is from an online forum(social networks). if you need more details or need sample of data , let me know.

I'm very new in this field ,so I have no idea. I do appreciate your help thanks I'm very new in this field ,so I have no idea. I do appreciate your help thanks

thanks for this information, Now, if the sequence is very long, how I can decide it has local similarity or overall similarity? I do appreciate your advise. thanks

hi, I'm PhD student, working in DNA sequence field , but with non biological data. my problem is : I don't know which alignment I have to use with my data global or local alignment what is I must depend on it to decide working with global or local. anyone need more details about my problem, let me know if you need sample of my data, I can send it I do appreciate any advise thanks