Answers.Body: <p>Besides generic nucleotide aligners, there are also more specialized tools for the alignment of 16S amplicon sequences, e.g. SINA (<a href="https://academic.oup.com/bioinformatics/article/28/14/1823/218226" rel="nofollow noreferrer" title="SINA article">article</a>, <a href="https://github.com/epruesse/SINA" rel="nofollow noreferrer" title="SINA at github">software</a>) which is part of <a href="https://www.arb-silva.de/" rel="nofollow noreferrer" title="SILVA website">SILVA</a></p>
  
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Answers.CreationDate: 2018-11-27T07:21:36.237Z
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Answers.UserDisplayName: Peter Menzel
Answers.Body: <p>As I understand, the software tool <a href="https://academic.oup.com/bioinformatics/article/30/17/i349/199474" rel="nofollow noreferrer">Lambda</a> is a viable, yet lesser known alternative to BLAST in the context of taxonomic classification of NGS data.</p>
  
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Answers.UserDisplayName: Michael Gruenstaeudl
Answers.Body: <p>Why not shift the parameter inputs of Blast to exclude the species/subspecies which are being queried? Happy to show you how to do it, but that will pick up homologues. Alternative parse the blast output for e.g. 20000 outputs using E or identity within the threshold required (that's the way I'd do it).</p>
  
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Answers.UserDisplayName: M__
Answers.Body: <p>All tools I’m aware of will be more-or-less as fast as blast. With kmer-based methods, the investment will be the up-front kmer database build.</p>
  
  <p>Not sure if you’ve tried this, but NCBI has a 16S microbial blast database (lots of species, 16S rRNA only) just for this purpose. No point to search millions of nts for the 16S sequence every time if you know it’s SOME 16S sequence, so limit the search to only16S sequences.</p>
  
  <p>I’d recommend you build a local blast database from <a href="ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz" rel="nofollow noreferrer">ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz</a></p>
  
  <p>BTW, another answer says blast won’t give you the alignment. Blast actually will give you alignments, you just have to ask it for that output format.</p>
  
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Answers.UserDisplayName: mRotten
Answers.Body: <p>You can give a try to this tool: <a href="https://www.dnaservic.es/" rel="nofollow noreferrer">dnaservic.es</a>
  It's actually available experimentaly. It is a real local aligner, not just a search tool like BLAST. It really returns an alignment. It is usually slower than BLAST, but bot much slower in most cases. In contrast it usually returns alignments with better scores and not only partial alignments.</p>
  
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Answers.UserDisplayName: juanjo75es
Body: <p>After some <a href="https://bioinformatics.stackexchange.com/questions/2846/why-does-a-very-strong-blast-hit-get-lost-when-i-change-num-alignments-num-desc">unexpected results</a> (and <a href="https://blastedbio.blogspot.com/2018/11/blast-max-alignment-limits-part-four.html" rel="nofollow noreferrer">previously reported</a>) I heard that there are other tools for finding similar sequences besides blast that are faster and more accurate.</p>
  
  <p>I only found <a href="http://hmmer.org/" rel="nofollow noreferrer">hmmer</a>, but I don't know if it is faster and more accurate.</p>
  
  <p>Is there any review comparing such tools? A quick google scholar search didn't report anything useful.</p>
  
  <p>I want to search with short DNA sequences (~400), mainly interested for taxonomic imputation so I'll be looking for similar sequences and not distant homologs. I won't try to model genes and the sequence will be unspliced as it is from direct sequencing of a a region of the 16S gene.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-26T12:11:32.673Z
Comments.Text: Please [edit] your question and give us more details about what you will be looking for. Will these be nucleotide queries? Protein? Will you be looking for very similar sequences or distant homologs? Long sequences? Short ones? These details will affect your choice of tool.
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2018-11-26T12:56:47.807Z
Comments.Text: My question is mainly theoretically, but I narrowed with the use case that prompted me to ask/think about this
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-26T13:12:23.620Z
Comments.Text: The thing is you have tools like blat and megablat, FASTA (although I doubt anyone uses that anymore), hmmer, cd-hit, psi-blast, etc. It's really hard to answer unless you give a specific usage scenario. For instance, will you be trying to model genes? Would you want a tool like exonerate or genewise that can align a spliced cDNA sequence to a genome? Or will your 400 sequences be unspliced?
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2018-11-26T13:24:50.637Z
Comments.Text: Ok, I realize this is more complicated than I thought. Thanks it is not my field/research focus :D. I updated the question with more information. Thanks for the guidance.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-27T01:10:28.973Z
Comments.Text: Try VSEARCH (or USEARCH). They are not BLAST replacement but can be a good choice for the right applications.
Comments.UserDisplayName: user172818
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Comments.CreationDate: 2019-02-12T00:47:46.893Z
Comments.Text: taxonomy assignment algorithms often use kmer-based methods which are faster than alignments (it looks like you are doing something like this?). You could just search for taxonomy assignment instead of alignment to find relevant alternative methods.
Comments.UserDisplayName: rrr
Tags: <phylogenetics><blast><literature-search>
Title: Fast and reliable alternatives to blast
ThreadText: # Fast and reliable alternatives to blast
  
  (Asked by: username_0 on 2018-11-26)
  
  After some [unexpected results](https://bioinformatics.stackexchange.com/questions/2846/why-does-a-very-strong-blast-hit-get-lost-when-i-change-num-alignments-num-desc) (and [previously reported](https://blastedbio.blogspot.com/2018/11/blast-max-alignment-limits-part-four.html)) I heard that there are other tools for finding similar sequences besides blast that are faster and more accurate.
  
  I only found [hmmer](http://hmmer.org/), but I don't know if it is faster and more accurate.
  
  Is there any review comparing such tools? A quick google scholar search didn't report anything useful.
  
  I want to search with short DNA sequences (~400), mainly interested for taxonomic imputation so I'll be looking for similar sequences and not distant homologs. I won't try to model genes and the sequence will be unspliced as it is from direct sequencing of a a region of the 16S gene.
  
  **Tags:** phylogenetics, blast, literature-search
  
  > **Comments:**
  > **username_1**: Please [edit] your question and give us more details about what you will be looking for. Will these be nucleotide queries? Protein? Will you be looking for very similar sequences or distant homologs? Long sequences? Short ones? These details will affect your choice of tool.  
  > **username_0**: My question is mainly theoretically, but I narrowed with the use case that prompted me to ask/think about this  
  > **username_1**: The thing is you have tools like blat and megablat, FASTA (although I doubt anyone uses that anymore), hmmer, cd-hit, psi-blast, etc. It's really hard to answer unless you give a specific usage scenario. For instance, will you be trying to model genes? Would you want a tool like exonerate or genewise that can align a spliced cDNA sequence to a genome? Or will your 400 sequences be unspliced?  
  > **username_0**: Ok, I realize this is more complicated than I thought. Thanks it is not my field/research focus :D. I updated the question with more information. Thanks for the guidance.  
  > **username_2**: Try VSEARCH (or USEARCH). They are not BLAST replacement but can be a good choice for the right applications.  
  > **username_3**: taxonomy assignment algorithms often use kmer-based methods which are faster than alignments (it looks like you are doing something like this?). You could just search for taxonomy assignment instead of alignment to find relevant alternative methods.  
  
  ---
  
  ## 5 answers
  
  ### Answer by username_4 on 2018-11-27. Score: 4
  
  Besides generic nucleotide aligners, there are also more specialized tools for the alignment of 16S amplicon sequences, e.g. SINA ([article](https://academic.oup.com/bioinformatics/article/28/14/1823/218226 "SINA article"), [software](https://github.com/epruesse/SINA "SINA at github")) which is part of [SILVA](https://www.arb-silva.de/ "SILVA website")
  
  
  ---
  
  ### Answer by username_5 on 2018-11-27. Score: 4
  
  As I understand, the software tool [Lambda](https://academic.oup.com/bioinformatics/article/30/17/i349/199474) is a viable, yet lesser known alternative to BLAST in the context of taxonomic classification of NGS data.
  
  
  ---
  
  ### Answer by username_6 on 2019-01-28. Score: 0
  
  Why not shift the parameter inputs of Blast to exclude the species/subspecies which are being queried? Happy to show you how to do it, but that will pick up homologues. Alternative parse the blast output for e.g. 20000 outputs using E or identity within the threshold required (that's the way I'd do it).
  
  
  ---
  
  ### Answer by username_7 on 2019-09-13. Score: 0
  
  All tools I’m aware of will be more-or-less as fast as blast. With kmer-based methods, the investment will be the up-front kmer database build.
  
  Not sure if you’ve tried this, but NCBI has a 16S microbial blast database (lots of species, 16S rRNA only) just for this purpose. No point to search millions of nts for the 16S sequence every time if you know it’s SOME 16S sequence, so limit the search to only16S sequences.
  
  I’d recommend you build a local blast database from <ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz>
  
  BTW, another answer says blast won’t give you the alignment. Blast actually will give you alignments, you just have to ask it for that output format.
  
  
  ---
  
  ### Answer by username_8 on 2019-09-10. Score: -2
  
  You can give a try to this tool: [dnaservic.es](https://www.dnaservic.es/)
  It's actually available experimentaly. It is a real local aligner, not just a search tool like BLAST. It really returns an alignment. It is usually slower than BLAST, but bot much slower in most cases. In contrast it usually returns alignments with better scores and not only partial alignments.
  
  
  ---
  
  