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Where can I find some datasets of aligned nucleotide sequences? And what should I assume about the accuracy of the alignments there?

(I would like to use such datasets for training the alignment model I am working on. In particular, to help me get an estimate on some parameters such as the frequency of single nt INDEL at some locations.)

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    $\begingroup$ What do you want to do with this aligned sequences? Test algorithms? Actually your question is a bit unclear. $\endgroup$ – Chris Aug 6 '14 at 11:35
  • $\begingroup$ I would like to use such a dataset for training, i.e. to help me infer some parameters for the alignment tool I am working on. Thank you for your comment; I will edit my question to clarify. $\endgroup$ – Anas Elghafari Aug 6 '14 at 11:45
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    $\begingroup$ I agree with @Chris! do you mean if the alignment itself can be trusted based on the algorithm used or the sequences themselves can be trusted. Are you worried about the semi-conserved sequences being aligned in a variable manner depending on the algorithm used? For different alignment algorithms please see this post (biology.stackexchange.com/questions/20075/…). I could be totally wrong but multiple alignment and semi-conserved sequences is mostly an issue for AA not nucleotides since they either match or they don't $\endgroup$ – Behzad Rowshanravan Aug 6 '14 at 11:46
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    $\begingroup$ Well.. Indels are read by your sequencer.. There are machine errors and sample prep errors. You have to set up controls in your machine and train your set.. I haven't really understood your question, however. $\endgroup$ – WYSIWYG Aug 6 '14 at 12:12
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    $\begingroup$ There are some manually curated HIV alignments at LANL. HIV is quite variable in length so you will find many indels in these alignments. $\endgroup$ – rmccloskey Sep 20 '14 at 1:51
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You can find 46-way multiz alignment from UCSC genome browser, it is down on comparative genomics part and labelled as "cons 46-way", which is a genome alignment of 46 vertebrate species. You can use data on their genome browser on the site, or get download information here.

If you are interested in pair-wise alignments, I don't know of any pair-wise alignment database, but in fact you don't need one. You can search for nucleotide sequences from NCBI nucleotide database and align them using BLAST on their website. BLAST is maybe the most common tool for pair-wise alignments and also for database alignment searches, where a single query sequence is searched for matches throughout a database of sequences. If you want to do a large number of alignments, you can download BLAST to your computer to do them faster.

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