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The Gene Indices Sequence Cleaning and Validation script (SeqClean) 0.Introduction 1.Requirements 2.Installation 3.Usage and methods 4.Copyright 5.Contact information 0.Introduction ============== SeqClean is a tool for validation and trimming of DNA sequences from a flat file database (FASTA format). SeqClean was designed primarily for "cleaning" of EST databases, when specific vector and splice site data are not available, or when screening for various contaminating sequences is desired. The program works by processing the input sequence file and filtering its content according to a few criteria: * percentage of undetermined bases * polyA tail removal * overall low complexity analysis * short terminal matches with various sequences used during the sequencing process (vectors, adapters) * strong matches with other contaminants or unwanted sequences (mitochondrial, ribosomal, bacterial, other species than the target organism etc.) The user is expected to provide the contaminant databases, they are not included in this package. 1.Requirements ============== * perl version >= 5.6 * a working installation of recent versions of NCBI's blastall and megablast programs ( * one or more databases of potential contaminants (e.g. a vector database like NCBI's UniVec) properly formatted to work with NCBI's blastall (using formatdb) A binary distribution for this package is provided for Linux ix86 systems with glibc >=2.1. NCBI's blastall and megablast are not included, they should instead be obtained directly from NCBI. The source code of the various other tools included in the package is provided so they can be compiled on other Unix platforms where NCBI's tools work. 2.Installation ============== Create a directory where you plan the package to reside. Copy the compiled archive into that directory and unpack the archive in there: tar xvfz seqclean.tar.gz This will unpack a few files in the current directory and will create a bin subdirectory with several files. The program to run is seqclean script from the main directory. When launched, this program will prefix the local ./bin subdirectory to the shell's path. Optionally, you may move/copy all binaries and scripts from ./bin subdirectory somewhere in your working shell PATH. You can also copy the main script (seqclean) to your preferred script location (which should be in the shell's PATH), in which case the module Mailer.pm should go in the same directory with the tgicl script or into a one of the PERLLIB (%INC) directories. There are 2 perl scripts in this package: seqclean bin/seqclean.psx They all have the perl location as the first line, set to #!/usr/bin/perl If this is not the valid path for your perl installation you need to change these lines in all three files, to point to your actual perl binary location. 3.Usage and methods =================== A short usage message is displayed when seqclean script is launched without any parameters. The seqclean script takes an input sequence file (fasta formatted) as the only required parameter: seqclean your_est_file seqclean creates two output files of interest: 1. the filtered FASTA file (your_est_file.clean for the example above) containing only valid (non-trashed) and trimmed ("clear range") sequences 2. a "cleaning report" (your_est_file.cln) providing details about sequence trimming and trashing (coordinates, reasons for trashing, contaminant names etc. - see below for a detailed description). However, the simple usage example above will not perform any searches against contaminant databases (as there are none specified) but it will only provide basic analysis, removing the polyA/polyT tail, possibly clipping low-quality ends (the ends rich in undetermined bases) and trashing the ones which are too short (shorter than 100 or the -l parameter value) or which appear to be mostly low-complexity sequence. As suggested in the "Introduction", the contaminant databases provided by the user can be considered to be of two types: 1. vector/adapter databases, which can determine the trimming of the analyzed sequences even when only very short terminal matches (down to 12 base pairs) are found. These database files should be provided with the -v option (vector detection) 2. extensive contaminants databases: the alignments between these contaminants and the analyzed sequences are only considered if they are longer than 60 base pairs with at least 94% identity; these are provided with the -s option (screening for contamination) In both cases the analyzed sequences will be searched against the provided files and the overlaps are analyzed. The contaminant databases should be all formatted as required for blastall (using NCBI's formatdb program). In the first case (vector/linker scan), the overlaps are only considered if they are above 92% identity, they have very short gaps and they are located in the 30% distance from either end. Also, the shorter these overlaps are, the closer to either end of the analyzed sequence they should be, in order to be considered for trimming of the target sequence. Multiple vector/adapter databases can be provided at the -v option, separated by comma (do not use spaces around the comma). Example: seqclean your_est_file -v /usr/db/UniVec,/usr/db/adaptors,/usr/db/linkers In this example three database files are checked for short terminal matches with the analyzed sequences from "your_est_file". The -s option case 2. above) works in a similar way, as more than one file can be provided, but in that case only larger, statistically more significant hits are considered. Example: seqclean your_est_file -v /usr/db/UniVec,/usr/db/linkers \ -s /usr/db/ecoli_genome,/usr/db/mito_ribo_seqs In both cases, the contaminant database files should be provided with their full path unless they can be found in the current working directory. The searches against "-v" files are performed using blastall (blastn) with low stringency, while for "-s" provided files, megablast is used, for very fast screening. By default, the "smart" low-complexity filter is used during both type of searches (the -F "m D" option of blastall/megablast). However, in some cases, short vector/adaptor terminal overlaps might be expected in regions of low-complexity, so the dust filter can be disabled completely for any database file given at the "-v" option, by appending the "^" character at the end of the file name: seqclean your_est_file -v /usr/db/adapters^,/usr/db/UniVec,/usr/db/linkers^ \ -s /usr/db/ecoli_genome,/usr/db/mito_ribo_seqs In the example above, the "dust" filter is totally disabled for blastn searches against /usr/db/adapters and /usr/db/linkers, while for the other files (/usr/db/UniVec) it will still be set to work in "smart" mode as mentioned above. The cleaning scripts keep track of iterative trimming of the input sequences through multiple matches with various contaminants, if that's the case.The 5' end (end5) coordinate of each input sequence is initially set to 1, and the 3' end (end3) coordinate is considered to be the length of the initial sequences. During the above mentioned trimming procedures, end5 can be increased and/or end3 can be decreased. The final end3-end5+1 range is considered to be the "clear range" of the sequence after going through the cleaning procedure. No matter if trimming was applied or not, if the "clear range" length is shorter than a minimum value (default 100nt, can be set by -l option), the sequence will be considered invalid and it will be trashed. Also, at the end of the cleaning procedure, the percentage of undetermined bases from the clear range is computed and the sequence is also trashed if this percentage is larger than 3%. Cleaning report format ---------------------- Each line in the cleaning report file (*.cln) has 7 tab-delimited fields as follows: 1. the name of the input sequence 2. the percentage of undetermined bases in the clear range 3. 5' coordinate after cleaning 4. 3' coordinate after cleaning 5. initial length of the sequence 6. trash code 7. trimming comments (contaminant names, reasons for trimming/trashing) The trash code field (6) should be empty if (part of) a sequence is considered valid - so it can be found in the final filtered file (*.clean) The trash code field will be set to the file name of the last contaminant database, if that determined the clear range to fall below the minimum value (-l parameter, default 100). There are three reserved values of the trash code: "shortq" - assigned when the sequence length decreases below the minimum accepted length (-l) after polyA or low quality ends trimming; "low_qual" - assigned when the percentage of undetermined bases is greater than 3% in the clear range; "dust" - assigned when less than 40nt of the sequence is left unmasked by the "dust" low-complexity filter; The reasons and the coordinates for trimming are mentioned in the 7th field. When trimming was due to a contaminant match, the contaminant name and the overlap coordinates are mentioned. When trimming was due to polyA tail or low quality ends removal, the "trimpoly" program name is mentioned along with the trimming coordinates. Besides the -s and -v parameters mentioned above, here is a brief summary of the other parameters: -c : enables parallel processing by specifying the number of local CPUs to use (for a SMP machine) or a filename containing a list of PVM node names (one host name per line, per CPU). In the PVM case, if a node is also a SMP machine and you want to use more than one CPU on that node, you should list that same node name as many times as many CPUs you want to use on that node. If this option is not provided, only one CPU is used on the local machine. -n : the input file is not usually processed as one single query file. Instead, it is sliced up into little parts and each part is processed separately; this option is useful to tweak when you also make use of the multi-CPU option (-c), as each slice can be processed by one CPU. -l : the minimum accepted length of the clear range in order to be considered valid. If the length of the clear range falls below this value, a trash code is assigned to the input sequence and it will be exclued from the output filtered file (*.clean) -r : custom name of the cleaning report file (default: add the ".cln" suffix to the input file name) -o : custom name of the final "clear range"-only FASTA file containing only the valid sequences (default: append ".clean" suffix to the input file name) -x : set the minimum percent identity to be considered for an alignment with a contaminant (default 96) -y : minimum length of a terminal vector hit to be considered (>11, default 11) -N : disable any attempt of trimming of low quality ends (ends rich in N = undetermined bases) -M : completely disable trashing of low quality (N-rich) sequences -A : disable trimming of polyA tails from 3' end or polyT from 5' end of the input sequences -L : disable low-complexity analysis and the trashing of input sequences by this criterion -I : do not rebuild the .cidx file (if already there) -m : enable sending of e-mail notification to the mentioned address, at the end of the cleaning process or in case of error If after seqclean one needs to trim the corresponding quality values too, according to the new coordinates or trash codes found by seqclean, the utility script "cln2qual" is included (see the usage message). It expects a fasta-like file containing space delimited quality values for each nucleotide of the original sequences. It should be run after the seqclean, as it parses the trimming ("clear range") coordinates and trash codes from the cleaning report and applies them to the quality records. 4.Copyright =========== Copyright (c) 2005-2006, Dana-Farber Cancer Institute, All Rights Reserved This software is OSI Certified Open Source Software. OSI Certified is a certification mark of the Open Source Initiative. 5.Contact information ===================== For problems or questions related to the tools included in this package please contact Geo Pertea at gpertea@jimmy.harvard.edu
Source: seqclean_README, updated 2010-07-22

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