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Percent identity BLAST

  1. the BLAST program. BLAST results have the following fields: E value: The E value (expected value) is a number that describes how many times you would expect a match by chance in a database of that size. The lower the E value is, the more significant the match. Percent Identity: The percent identity is a number that describes how similar the quer
  2. When I use web-BLAST, I just get Identity % but not the similarity %. Is there any command which could be used to get both Identity % and similarity % during BLAST analysis? ADD REPLY • link 4.9 years ago by hnp21 ▴ 4
  3. Percent Identity describes how similar the query is to the aligned sequences It is not really possible to make an informed decision about the scores, or the validity of the alignments, without..
  4. o acid sequence. Ident[ity]: the highest percent identity for a set of aligned segments to the same subject sequence
  5. The Basic Local Alignment Search Tool (BLAST) finds regions of similarity between sequences. The program compares nucleotide or protein sequences and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families

The BLAST nucleotide sequence identity suggested 75-98% relationship or similarity, depending on the fungi type. Thus, I think some of the organisms are novel. I have found some references that.. The percentage identity for two sequences may take many different values. It is dependent on: The method used to align the sequences. e.g. BLAST, FASTA, Smith-Waterman implemented in different programs, Global alignment (implemented in different programs), structural alignment from 3D comparison. etc. etc. etc QuickBLASTP is an accelerated version of BLASTP that is very fast and works best if the target percent identity is 50% or more. BlastP simply compares a protein query to a protein database. PSI-BLAST allows the user to build a PSSM (position-specific scoring matrix) using the results of the first BlastP run

Thus, the NCBI Blast web site uses a color code of blue for alignment with scores between 40-50 bits; and green for scores between 50-80 bits. In the yeast vs human example, the alignments with less than 20% identity had scores ranging from 55 - 170 bits Sequence identity is the amount of characters which match exactly between two different sequences. Hereby, gaps are not counted and the measurement is relational to the shorter of the two sequences. This has the effect that sequence identity is no.. Percent identity is defined as the percent of the sequences that have identical residues at the same alignment positions and is calculated by the number of identical residues divided by the length of the alignment multiplied by 100 (100* (hsp_identity/hsp_align-len)) BLAST (Basic Local Alignment Search Tool) was developed in 1989 at the National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH). score, query coverage (percent of the query sequence that overlaps the subject sequence), E-value (see below), and max identity (percent similarity between the query and.

MLA CE Course Manual: Molecular Biology Information

BLAST: Identity % and Similarit

Using BLAST to perform a pairwise alignment, we see that 100 amino acids are identical. % identity is Identity = 100 / 320 = 31.25%. We always use the smaller sequence length as the denominator. Additionally, we see that there are 23 amino acids that are different by conservation substitution, meaning that their chemical properties are maintained Percent identity: the % of bases that are identical to the reference genome. A query sequence can have a low % identity, but still be a real hit. It is essential to take the e value into account and look for homology between conserved regions- this will be evident at the protein level. Click on the Alignments tab BLAST identity. BLAST identity is defined as the number of matching bases over the number of alignment columns. In this example, there are 50 columns, so the identity is 43/50=86%. In a SAM file, the number of columns can be calculated by summing over the lengths of M/I/D CIGAR operators what is the percent identity and query coverage? identity: 74% and query coverage: 76% what is the E-value? 5e-50 (meaning 5×10-50) are there any gaps in the alignment? Yes, there are exactly the same gaps as in the previous question. QUESTION 1.4. What are the sizes (in basepairs) of the databases we used for the two BLAST searches

How to Interpret BLAST Results

Basic Local Alignment Search Tool (BLAST) (1, 2) is the tool most frequently used for calculating sequence similarity. BLAST comes in variations for use with different query sequences against different databases. All BLAST applications, as well as information on which BLAST program to use and other help documentation, are listed on the BLAST. The traditional BLAST databases are available through the pull-down list once the Others (nr etc.) radio button is selected. Percent Query Coverage, and Maximum Percent Identity. The Box below provides definitions for these metrics. Sorting options are also available for multiple hits within the alignments for each subject (database. 9. In the BLAST report generated from the search, scroll to the Descriptions table. Find the Percent Identity (Per. Ident) column. Percent identity values indicate how well the . HBB. gene sequences of the listed species match with the . HBB. gene sequence of Species A. Notice how the first 100 results return a 100% Percent Identity. Percent identity vs. alignment score quartile plot for the proline racemase superfamily (IPR008794). Example 2: multidomain proteins In a more complicated situation, the polypeptides of homologous members of the vicinal oxygen chelate superfamily (VOC; IPR004360) can be either a single domain or two tandemly fused homologous copies of the same.

In [9]: hits = blast_record. getHits (percent_identity = 90, percent_overlap = 70) In [10]: list (hits) Out[10]: ['1mkp'] This results in only MKP-3 itself, since percent_identity argument was set to 90 Note that we have only extracted a very small amount of information from the BLAST output (name of the query sequence, name of the top hit sequence, and percent identity of the top hit). But depending on your needs, you can extract essentially any of the information you could want from the file, including alignment lengths, positions. BLAST Terminology Definitions To understand the conversion of a BLAST pident to the full length percent identity used as a cutoff in TaxAss, first you must understand the BLAST terminology. Below are some basic BLAST terms: Query The sequence you input into BLAST (here, an OTU sequence Primer-BLAST was designed to make primers that are specific to an input PCR template, using Primer3. It can also check user supplied primers for specificity. The Search for short, nearly exact matches nucleotide and protein pages no longer exist The most effective similarity searches compare protein sequences, rather than DNA sequences, for sequences that encode proteins, and use expectation values, rather than percent identity, to infer homology. The BLAST and FASTA packages of sequence comparison programs provide programs for comparing protein and DNA sequences to protein databases.

Using BLAST in the cloud environment cloud is an ideal solution to this dilemma. The BLAST databases have also been moved to the cloud allowing you to run computations close to where the data is, eliminating the time and resources needed to download large data files to your local network 4.6.2.6 perc_identity: Minimum percent identity of matches to report . 4.6.2.7 dust: Arguments to DUST filtering algorithm (use 'no' to disable). 4.6.2.8 filtering_db: Name of BLAST database containing filtering elements (i.e.: repeats) 4.6.2.9 window_masker_taxid: Enable WindowMasker filtering using a Taxonomic ID [experimental Is BLAST the right algorithm for this or something else? The context is that a certain patent protects all sequences at least 90% or more identity to a given sequence. I wanted to test some candidate sequences and verify the percent identity metric. Below I post a patent-snippet where they actually define their identity metric

Genomic DNA sequence: most estimates of percent identity between humans and chimpanzees put the full genomic percent identity at 98-99%, although estimates as low as 95% have been put forth when including insertions and deletions and a recent study comparing the completed genomes of the two found a 96% identity Percent Identity: Each blast hit is colored based on its percent identity. The colors are displayed in a green-yellow-red gradient with green being the top score and red being the bottom score. An example of such colors are show for Log Quality Sets a range of acceptable deviation from the highest percent identity hit (Decimal value) in which a more detailed definition would be prefered. Must order by percent identity to use this functionality. Code Example. Running BLAST-QC on a sample result file (replicating -max_target_seqs 1)

BLAST Results - Introduction to NCBI Bioinformatics

The typical threshold for a good E−value from a BLAST search is e−5=(10−5) or lower. • 1. The reason for such low values is that an E=0.001 in a million entry database would still leave 1000 entries due to chance. An E=e−6 would only leave one entry due to chance. The percentage of identity for this sequence alignment is simply 4/12, or 30%. Then, the score of the alignment can be assessed, for example, by a simple expression: (Score) S= number of matches - number of mismatches = 4 - 12 =- Identity (B,C)=100%, but identity (A,C)=85% ((6 identical nucleotides / 7)). Similarity is the degree of resemblance between two sequences when they are compared. This is dependent on their identity. It shows the extent to which residues in aligned Definitions of identity vary depending on the treatment of gaps. Some popular definitions of %id Terminal gaps are ignored; identity is calculated from the remaining columns. An identity is a column with two identical letters; a mismatch is a column with two different letters

Percent Identity Matrix - created by Clustal2.1. 1: PF3D7_1454400 100.00 16.18 20.35 2: gi|5902181|gb|AAD01211.2| 16.18 100.00 29.66 3: S000001586 20.35 29.66 100.00 My doubts: I would like to know how to interpret this matrix result; Coming back to sequence alignments results, when I click on 'Show colors', the alignment summary is colored in. The most effective similarity searches compare protein sequences, rather than DNA sequences, for sequences that encode proteins, and use expectation values, rather than percent identity, to infer homology. The BLAST and FASTA packages of sequence comparison programs provide programs for comparing protein and DNA sequences to protein databases. percentage_identity(): A fast method for calculating the average percentage identity of the alignment; consensus_iupac(): Making a consensus using IUPAC ambiguity codes from DNA and RNA. Aligning 2 sequences with Blast using bl2seq and AlignIO. As an alternative to Smith-Waterman,. The percentage used was appended to the name, giving BLOSUM80 for example where sequences that were more than 80% identical were clustered. BLOSUM r: the matrix built from blocks with less than r% of similarity - E.g., BLOSUM62 is the matrix built using sequences with less than 62% similarity (sequences with ≥ 62% identity were clustered.

BLAST: Compare & identify sequences - NCBI Bioinformatics

Alignment as extended BTOP string This is the same BTOP string as in BLAST tabular output with a few extensions: a number represents this many matches, two bases represent a mismatch and show query and reference base, base and gap or gap and base, show a gap in query or reference, ^<number>^ represents an intron of this number of bases Database against which the search is performed: UniProtKB or clusters of sequences with 100%, 90% or 50% identity. Threshold: The expectation value (E) threshold is a statistical measure of the number of expected matches in a random database. The lower the e-value, the more likely the match is to be significant Wilson et al. showed that percent identity in sequence alignment is more effective at quantifying functional conservation of their simple classification of SCOP domains than modern probabilistic scores [ 22 ]. However, all these studies did not use a broad definition of functions for a systematic large-scale analysis percentage of identical matches 4. length alignment length 5. mismatch number of mismatches 6. gapopen number of gap openings 7. qstart start of alignment in query 8. qend end of alignment in query 9. sstart start of alignment in subject 10. send end of alignment in subject 11. evalue expect value 12. bitscore bit scor

What should be the minimum percent of identity and

A. Percent of nucleotides or amino acids that are identical between two sequences. If a BLAST search returns a match with an E-value of 1 e-20, and 200 searches without alignment have an average percent identity of 25%. How would the average . Name holman_final formatted 11.07.04 11/14/2004 3:27 pm 55 protein similarity score: a simplified version of the blast score as a superior alternative to percent identity for claiming genuses of related protei Christopher M. Holman,Protein Similarity Score: A Simplified Version of the Blast Score as a Superior Alternative to Percent Identity for Claiming Genuses of Related Protein Sequences , 21Santa Clara High Tech. L.J.55 (2004) • BLAST: you can now press the BLAST button to get to the results. However, if you find that you need more results to find more similar species, re-do your search but press Algorithm parameters located underneath the BLAST button and increase the number of results from the default 100 to 250 or even 500. 5

E-value can be used as a first quality filter for the BLAST search result, to obtain only results equal to or better than the number given by the -evalue option. Blast results are sorted by E-value by default (best hit in first line). blastn -query genes.ffn -subject genome.fna -evalue 1e-10 The smaller the E-value, the better the match Let's say that you have a fasta file called seqs.fasta, and you want to run a blast against the nucleotide database (nt) located on you home folder (/home/user). You want to restrict your blast to an evalue of 1E-10, a percent id of 95%, and retrieve only 50 target sequences that have a query coverage of over 90% No single characteristic identifies a blast. In general, blasts are cells that have a large nucleus, immature chromatin, a prominent nucleolus, scant cytoplasm and few or no cytoplasmic granules. Blasts may not have all of these features. Cell size - blasts are often medium to large cells In the Alignment section, percent identity is given above each alignment; for example, Identities = 563/564 (99%). This is the number of amino acids that are identical in each protein. Add a column for BLAST % difference. You can calculate this as 100% identical (for example, 99% identity = 1% difference) similarity search in high-quality scientific databases and software tools using Expasy, the Swiss Bioinformatics Resource Portal

or upload a file: Project ID (required) --prot_emax - maximum BLAST expect value for protein genes --prot_pmin - minimum percent identity for protein gene Make nucleotide overlaps at VDJ junctions an option (-allow_vdj_overlap) and default is set to no o verlap allowed. Previous versions were hard-coded to allow nucleotide overlaps at VDJ junctions. *Use alignment length instead of percent identity as tiebreaker for hits with identical blast scores . Allow custom J gene mismatch penalty DNA Learning Center Barcoding 101 includes laboratory and supporting resources for using DNA barcoding to identify plants or animals. Research programs enable high school students and teachers to gain an intuitive understanding of the interdependence between humans and the natural environment

What is the acceptable percentage similarity of BLAST

  1. ppos Percentage of positive-scoring matches frames Query and subject frames separated by a '/' qframe Query frame sframe Subject frame btop Blast traceback operations (BTOP) staxids Subject Taxonomy ID(s), separated by a ';' sscinames Subject Scientific.
  2. The canonical clustering threshold is 97% identity, which was proposed in 1994 when few 16S rRNA sequences were available, motivating a reassessment on current data. Results Using a large set of high-quality 16S rRNA sequences from finished genomes, I assessed the correspondence of OTUs to species for five representative clustering algorithms.
  3. Introduction Protein sequence alignments in twilight zone. Protein sequences fold into unique three-dimensional (3D) structures. However, proteins with similar sequences adopt similar structures (Zuckerkandl and Pauling, 1965; Doolittle, 1981; Doolittle, 1986; Chothia and Lesk, 1986).Indeed, most protein pairs with more than 30 out of 100 identical residues were found to be structurally.
  4. 7. What is the percent identity and percent positives (aka percent similarity) of the . Bubalus. bubalis. leptin sequence compared to the human sequence? 8. How many hits came out of this search? Are all of them significant matches? Does the BLAST result support the hypothesis that chimps have a homolog of the human . leptin. gene? 9
  5. o acid residues are to one another
  6. g Genuses of Related Protein Sequences, 21 Santa Clara High Tech. L.J. 55 (2004)

Wikiomics:Percentage identity - OpenWetWar

  1. L11 Exercise B: BLAST and Align within MEGA 1. Launch MEGA web browser TASK MEGA has a built-in web browser that we will use to find and retrieve sequences. Follow the menu Alignment > Do BLAST Search to launch the internal browser that goes directly to NCBI BLAST. 2. BLAST search within MEGA 2.1. Paste sequence TASK Paste the query sequenc
  2. imum percentage identity of a BLAST hit for it to be taken into account in the analysis. - Maximum distance between genes in locus: this allows you to specify how far apart genes with a Blast hit are allowed to be to be counted as a single genomic locus.
  3. The calculation of percent identity for use in database selection is based on the percent identity returned by the National Center for Biotechnology Information's Basic Local Alignment Search Tool (BLAST) . The default megablast settings are appropriate for our application because they have been highly optimized to find short, highly similar.
  4. The top left panel of the BLAST results page shows the parameters used in the BLAST search (e.g., database name, query ID, query length). The controls in the top right panel can be used to filter the BLAST hits by organism, percent identity, and Expect value (E-value). The details o
  5. The new results incorporate feedback from surveys and interviews with BLAST users. We think you'll find the new results are more compact, easier to navigate, and expose useful formatting and other features that you may not have known about. The results page has organism, percent identity, and E value filters in plain view and easily accessible
  6. Sequence identity of each mutated sequence compared to the original and the BLAST output was evaluated using a Perl script written by this author. The 2013 study performed by this author was repeated for all chromosomes using version 2.2.25+ of the BLASTN algorithm with the parameters described above and a sequence slice of 300 bases
  7. ed as the best reciprocal hits that covered at least 50% of the sequence and had 10% sequence identity according to BLAST alignment. Genomic fluidity: Genomic fluidity measures the percentage of genes shared by two genomes. It is.

Searching for similarities between biological sequences is the principal means by which bioinformatics contributes to our understanding of biology. Of the various informatics tools developed to accomplish this task, the most widely used is BLAST, the basic local alignment search tool. This article discusses the principles, workings, applications and potential pitfalls of BLAST, focusing on the. BLAST (basic local alignment search tool) will show similar sequences that have been deposited to the NCBI sequence database, starting with the sequence with the highest similarity. Take a look at the results, noting the source of each sequence (in the name) and the percent identity (how many nucleotides within the sequence are the same. variety of blast hit metrics (length, e-value, score, percent ID, quality) find the closest genomic feature in the searched organisms Visualize individual hits in their genomic context to determine the extent to which you query matche The Percentage of identity: This gives you a concrete substitute for the E-value. An identity of more than 25 percent is good news. ( The identity is the number of identical residues divided by the number of matched residues — gaps are simply ignored. 12.2.1 BLAST hit table. The Grade column is a percentage calculated by Geneious by combining the query coverage, e-value and identity values for each hit with weights 0.5, 0.25 and 0.25 respectively. This allows you to sort hits such that the longest, highest identity hits are at the top..

I want to calculate the percentage identity between the two rows in this alignment. row = align[:,n] allows for the extraction of individual columns that can be compared. Columns that contain only - should not be counted Note the default residue is C and the percent identity levels that are displayed are from 90 to 10% in intervals of 10%; a residue is counted as conserved if it occurs with ≥80% identity. The HMMs tab provides the HMM for each cluster containing greater than the specified Minimum Node Count

The overall chromosomal average was only 73%, with average chromosomal identity varying between 68 and 78%. Individual alignment identity across the whole genome varied between 51 and 100% In the 30-50% identity range, errors can be more severe and are often located in loops. Below 30% identity, serious errors occur, sometimes resulting in the basic fold being mis-predicted

Protein BLAST: search protein databases using a protein quer

Pairwise Sequence Alignment is used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).. By contrast, Multiple Sequence Alignment (MSA) is the alignment of three or more biological sequences of similar length. From the output of MSA applications, homology can be inferred and the. The BLAST algorithm complies a list of Words typically of three AA (for protein search). Words at or above a threshold value T are defined as: A) Hits and are used to scan a database for exact matches that may then be extende The similarity score is essentially a modified version of the BLAST score, a standard approach used by biologists to measure the degree of structural similarity between related protein sequences. The primary advantage of the similarity score approach compared to conventional protein claiming techniques, such as by percent identity or. Using BLAST to compare sequences to a sequence database. By the end of 2002 the GenBank database had over 28x10 9 base pairs of DNA sequence data. Some of this has been annotated, but much of it either has no annotations or is incorrectly annotated. What percent sequence identity would you expect in an alignment (without gaps) of two random. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. (Reference:P. Somervuo & L. Holm. 2015

Use alignment length instead of percent identity as the tie-breaker for hits with identical blast scores, improving accuracy in the V, D, J gene assignment. IgBLAST was developed at the NCBI to facilitate the analysis of immunoglobulin and T cell receptor variable domain sequences -size [1020] Genome chunk size. -coverage [70] (0-100) Percentage of query coverage cutoff. -pid [30] (0-70) Percent identity cutoff for BLAST search results. Examples. Place the genomes you wish to compare in fasta format into a folder. An email address is required for calls to the NCBI servers

The percent identity value is a single numeric score determined for each pair of aligned sequences. It measures the number of identical residues (matches) in relation to the length of the alignment. As displayed in the matrix (PIM), real numbers show 2 decimal points Or one can use MEGABLAST with a relaxed percent identity cutoff (default set at 99%). Nucleotide-nucleotide searches are not the recommended way to find homologous protein coding regions in other organisms

Idenity, e value or bitscor

What is the difference between the percentage similarity

Title: 10e-PCR-ID-BLAST Author: Eby Bassiri Created Date: 5/1/2013 1:31:50 A Ident and Sim accepts a group of aligned sequences (in FASTA or GDE format) and calculates the identity and similarity of each sequence pair. Identity and si.. Hint: Refer to the BLAST tutorial to find an overview of the GenBank nucleotide record. If sequences from more than one organism match your query, use the E value, the % identity and fraction of the query matched to determine the best match. If all the nucleotides in a sequence match, the % identity will be 100%. If the quer stringency of the BLAST e-value cutoff for protein genes by decreasing it to 1e-6, and it will show tRNA and rRNA hits according to the default e-value (1e-3) and percent identity (70%) cutoffs but require a minimum match length of 50 nt: $ ./mitofy.pl --prot_emax=1e-6 --rna_mlen=50 legume.fasta Mazzy 3 CURRENCY EQUIVALENTS (as of 20 December 2017) Currency Unit CNY1.00 $1.00 - yuan (CNY) = $ 0.1514 = CNY6.6036 ABBREVIATIONS ADB APC BA BF BS EN CEN CF

BLAST-QC: automated analysis of BLAST results

Basic local alignment search tool (blast) 6.2 Alignments. Score, E-value, and percent identity always appear here. Depending on the program, percent positive scoring, P-value, group, gaps, strand, and reading frame may also be reported. Coordinates 62% identity. •All BLOSUM matrices are based on observed alignments; they are not extrapolated from comparisons of closely related proteins. •BLOSUM 62 is the default matrix in BLAST (the database search program). It is tailored for comparisons of moderately distant proteins. Alignment of distan [BiO BB] ParseBlastXmlReport in InterProScan 4.2 Robert Bukowski bukowski at tc.cornell.edu Tue May 9 11:58:03 EDT 2006. Previous message (by thread): [BiO BB] Percentage sequence identity calculation program Next message (by thread): [BiO BB] Call for Talk Abstracts/Papers: 2006 International Workshop on Multiscale Biological Imaging, Data Mining and Informatics, Santa Barbara, Sept 7-8, 200

Pairwise Alignment - Snipcadem

A guide to BLAST - IDseq Help Cente

For this, all predicted protein-coding sequences from the query genome were searched against the genomic sequence of the reference genome and were considered conserved when they had a BLAST match that was at least 60% of the overall sequence identity (recalculated to an identity along the entire sequence) and an alignable region > 70% of the. determine species' identity of unknown samples, a method known as ''barcoding'' (Hebert et al., 2003a, b). It is now similar queries can be done with the Blast Search option in threshold value and the criticisms about using a percent sequence difference to indicate possible new species (Morit

The user can select a database of choice and modify BLAST options(E-value, percent identity, query_coverage, number of hits to return). The BLAST results are provided in both tabular format and alignment format (standard BLAST output file) As a valued partner and proud supporter of MetaCPAN, StickerYou is happy to offer a 10% discount on all Custom Stickers, Business Labels, Roll Labels, Vinyl Lettering or Custom Decals. StickerYou.com is your one-stop shop to make your business stick. Use code METACPAN10 at checkout to apply your discount Use sequence statistics, rather than percent identity or percent similarity, as your primary criterion for sequence homology. 4. Check that the statistics are likely to be accurate by looking for the highest-scoring unrelated sequence, using prss3 to confirm the expectation, and searching with shuffled copies of the query sequence [randseq.

On the definition of sequence identity - GitHub Page

The key difference between similarity and identity in sequence alignment is that similarity is the likeness (resemblance) between two sequences in comparison while identity is the number of characters that match exactly between two different sequences.. Bioinformatics is an interdisciplinary field of science that mainly involves molecular biology and genetics, computer science, mathematics. A new emm type is dictated by: < 92% identity to a reference emm type (e.g., types emm1.0, emm2.0, emm3.0). Interruption of the reference open reading frame by >7 codons. Penalty of 0.5% subtracted from overall percentage identity score for each out of frame codon

The key difference between homology and similarity in bioinformatics is that homology refers to a statement about common evolutionary ancestry of two sequences whilst similarity refers to the degree of likeness between two sequences.. Bioinformatics is a field of science that combines biology, information engineering, computer science, mathematics and statistics to analyze and interpret. PSI-Blast (Protein Sequences Only) Searching with the plant globin sequence, Blastp gives 388 hits; number 166 is with human beta globin: NP000509.1 hemoglobin, beta 0.094 The E-value 0.094 means that a match of this score with an unrelated sequence would occur about 10% of the time. Results of PSI-Blast iteration 1 (391 hits) include of GSI of all bacterial relationships increased with 16S percent identity indicating inconsistencies between 16S percent identity and genome similarity. At a 16S percent identity of 97%, genome similarity ranged from 49% to 100%. In addition, we analyzed the relationship between current biological taxonomic classifications (phylum, class

(PDF) GDNF Overexpression from the Native Locus RevealsGenome-scale comparison and constraint-based metabolicMetagenomic islands of hyperhalophiles: the case of
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