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https://github.com/rcedgar/reseek

Protein structure alignment and search algorithm
https://github.com/rcedgar/reseek

bioinformatics bioinformatics-algorithms bioinformatics-tool computational-biology protein-sequences protein-structure search-algorithm

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Protein structure alignment and search algorithm

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README 

        
![Reseek](http://drive5.com/images/reseek_logo.jpg)



![Reseek](https://drive5.com/images/reseek_v2.3_fixed.jpg)



[Reseek](http://drive5.com/reseek) is a protein structure search and alignment algorithm which improves sensitivity in protein homolog detection

compared to state-of-the-art methods including DALI, TM-align and Foldseek with similar speed to Foldseek.



Reseek is based on sequence alignment where each residue in the protein backbone is represented by a 

letter in a novel “mega-alphabet” of 85,899,345,920 (∼1011) distinct states.



Method sensitivity was measured on the SCOP40 benchmark using superfamily as the truth standard, focusing

on the regime with false-positive error rates <10 per query, corresponding to E<10 for an ideal E-value.



[](https://www.youtube.com/watch?v=BzIgqdm9xDs)

![Reseek](https://drive5.com/images/reseek_readme.jpg)



### Command line


  -search        # Alignment (e.g. DB search, pairwise, all-vs-all)

  -convert       # Convert file formats (e.g. create DB)

  -alignpair     # Pair-wise alignment and superposition



Search against database

    reseek -search STRUCTS -db STRUCTS -output hits.txt

                 # STRUCTS specifies structure(s), see below



Recommended format for large database is .bca, e.g.

    reseek -convert /data/PDB_mirror/ -bca PDB.bca



Align and superpose two structures

    reseek -alignpair 1XYZ.pdb -input2 2ABC.pdb

           -aln FILE     # Sequence alignment (text)

           -output FILE  # Rotated 1XYZ (PDB format)



All-vs-all alignment

    reseek -search STRUCTS -output hits.txt



Output options for -search

   -aln FILE     # Alignments in human-readable format

   -output FILE  # Hits in tabbed text format

   -columns name1+name2+name3...

                 # Output columns, names are

                 #   query   Query label

                 #   target  Target label

                 #   qlo     Start of aligment in query

                 #   qhi     End of aligment in query

                 #   tlo     Start of aligment in target

                 #   thi     End of aligment in target

                 #   ql      Query length

                 #   tl      Target length

                 #   pctid   Percent identity of alignment

                 #   cigar   CIGAR string

                 #   evalue  You can guess this one

                 #   aq      AQ (aln. qual., 0 to 1, >0.5 suggests homology)

                 #   qrow    Aligned query sequence with gaps (local)

                 #   trow    Aligned target sequence with gaps (local)

                 #   qrowg   Aligned query sequence with gaps (global)

                 #   trowg   Aligned target sequence with gaps (global)

                 #   std     query+target+qlo+qhi+ql+tlo+thi+tl+pctid+evalue

                 # default aq+query+target+evalue



Search and alignment options

  -fast, -sensitive or -verysensitive     # Required

  -evalue E      # Max E-value (default 10 unless -verysensitive)

  -omega X       # Omega accelerator (floating-point)

  -minu U        # K-mer accelerator (integer)

  -gapopen X     # Gap-open penalty (floating-point >= 0)

  -gapext X      # Gap-extend penalty (floating-point >= 0)

  -dbsize D      # DB size (nr. chains) for E-value (default actual size)



Convert between file formats

    reseek -convert STRUCTS [one or more output options]

           -cal FILENAME    # .cal format, text with a.a. and C-alpha x,y,z

           -bca FILENAME    # .bca format, binary .cal, recommended for DBs

           -fasta FILENAME  # FASTA format



Create input for Muscle-3D multiple structure alignment:

    reseek -pdb2mega STRUCTS -output structs.mega



STRUCTS argument is one of:

   NAME.cif or NAME.mmcif     # PDBx/mmCIF file

   NAME.pdb                   # Legacy format PDB file

   NAME.cal                   # C-alpha tabbed text format with chain(s)

   NAME.bca                   # Binary C-alpha, recommended for larger DBs

   NAME.files                 # Text file with one STRUCT per line,

                              #   may be filename, directory or .files

   DIRECTORYNAME              # Directory (and its sub-directories) is searched

                              #   for known file types including .pdb, .files etc.



Other options:

   -log FILENAME              # Log file with errors, warnings, time and memory.

   -threads N                 # Number of threads, default number of CPU cores.




#### Build from source on Linux x86


cd src/; chmod +x build_linux_x86.bash ; ./build_linux_x86.bash




#### Build from source on OSX x86


cd src/ ; chmod +x build_osx_x86.bash ; ./build_osx_x86.bash




#### Build from source on Windows

Load `reseek.vcxproj` into Microsoft Visual Studio and use the Build command.



#### Static link warning

Don't worry about a warning something like this, it's expected:


warning: Using 'dlopen' in statically linked applications requires

  at runtime the shared libraries from the glibc version used for linking



### More documentation



[https://drive5.com/reseek](https://drive5.com/reseek)



### Reference



Edgar, Robert C. (2024) "Sequence alignment using large protein structure alphabets improves sensitivity to remote homologs" [https://www.biorxiv.org/content/10.1101/2024.05.24.595840v2](https://www.biorxiv.org/content/10.1101/2024.05.24.595840v2)



### SCOP40 benchmark code and results



https://github.com/rcedgar/reseek_bench